diff --git a/README.ja.md b/README.ja.md
index 67d425260..0d01ba175 100644
--- a/README.ja.md
+++ b/README.ja.md
@@ -178,7 +178,19 @@ bash start.sh
 
 ---
 **注意**: アプリケーションを実行する前に、すべての前提条件がインストールされ、環境変数が適切に設定されていることを確認してください。
-長期間更新がない場合は、プロジェクト内のデータベースファイル(`lancedb/`、`valuecell.db`、`.knowledgebase/`)を削除してから再起動できます。
+長期間更新がない場合は、ローカルデータを削除して再起動できます：
+- LanceDB ディレクトリ（システムアプリディレクトリに保存。`.env` と同じ場所）：
+  - macOS: `~/Library/Application Support/ValueCell/lancedb`
+  - Linux: `~/.config/valuecell/lancedb`
+  - Windows: `%APPDATA%\\ValueCell\\lancedb`
+- Knowledge ディレクトリ（システムアプリディレクトリに保存。`.env` と同じ場所）：
+  - macOS: `~/Library/Application Support/ValueCell/.knowledge`
+  - Linux: `~/.config/valuecell/.knowledge`
+  - Windows: `%APPDATA%\\ValueCell\\.knowledge`
+- SQLite データベースファイル（システムアプリディレクトリに保存。`.env` と同じ場所）：
+  - macOS: `~/Library/Application Support/ValueCell/valuecell.db`
+  - Linux: `~/.config/valuecell/valuecell.db`
+  - Windows: `%APPDATA%\\ValueCell\\valuecell.db`
 
 
 # 開発者
diff --git a/README.md b/README.md
index 33394e5bc..381fa92af 100644
--- a/README.md
+++ b/README.md
@@ -181,7 +181,19 @@ Once the application is running, you can explore the web interface to interact w
 - To ensure your account safety, you need to reset your API keys regularly. 
 
 ---
-**Note**: Before running the application, ensure all prerequisites are installed and environment variables are properly configured. If it has been a long time since the last update, you can delete the database files in the project directories: `lancedb/`, `valuecell.db`, `.knowledgebase/` and start fresh
+**Note**: Before running the application, ensure all prerequisites are installed and environment variables are properly configured. If it has been a long time since the last update, you can delete local data stores and start fresh:
+- LanceDB directory (stored in your system application directory):
+  - macOS: `~/Library/Application Support/ValueCell/lancedb`
+  - Linux: `~/.config/valuecell/lancedb`
+  - Windows: `%APPDATA%\ValueCell\lancedb`
+- Knowledge directory (stored in your system application directory):
+  - macOS: `~/Library/Application Support/ValueCell/.knowledge`
+  - Linux: `~/.config/valuecell/.knowledge`
+  - Windows: `%APPDATA%\ValueCell\.knowledge`
+- SQLite database file (stored in your system application directory):
+  - macOS: `~/Library/Application Support/ValueCell/valuecell.db`
+  - Linux: `~/.config/valuecell/valuecell.db`
+  - Windows: `%APPDATA%\ValueCell\valuecell.db`
 
 # Developers
 
diff --git a/README.zh.md b/README.zh.md
index 640c3e7ef..ea56ba504 100644
--- a/README.zh.md
+++ b/README.zh.md
@@ -182,7 +182,19 @@ bash start.sh
 ---
 
 **注意**：运行应用程序前，请确保所有前提条件已安装且环境变量已正确配置
-如长时间没有更新可以删除项目中数据库文件`lancedb/`,`valuecell.db`, `.knowledgebase/`再进行启动
+如长时间没有更新，可以删除本地数据并重新启动：
+- LanceDB 目录（位于系统应用目录，与 `.env` 同路径）：
+  - macOS: `~/Library/Application Support/ValueCell/lancedb`
+  - Linux: `~/.config/valuecell/lancedb`
+  - Windows: `%APPDATA%\\ValueCell\\lancedb`
+- 知识目录（位于系统应用目录，与 `.env` 同路径）：
+  - macOS: `~/Library/Application Support/ValueCell/.knowledge`
+  - Linux: `~/.config/valuecell/.knowledge`
+  - Windows: `%APPDATA%\\ValueCell\\.knowledge`
+- SQLite 数据库文件（位于系统应用目录，与 `.env` 同路径）：
+  - macOS: `~/Library/Application Support/ValueCell/valuecell.db`
+  - Linux: `~/.config/valuecell/valuecell.db`
+  - Windows: `%APPDATA%\\ValueCell\\valuecell.db`
 
 
 # 开发者
diff --git a/README.zh_Hant.md b/README.zh_Hant.md
index 5444231fe..812dde29c 100644
--- a/README.zh_Hant.md
+++ b/README.zh_Hant.md
@@ -179,7 +179,19 @@ bash start.sh
 ---
 
 **注意**：啟動應用程式前，請確認所有前置條件已安裝且環境變數正確設定。
-若長時間未有更新，可以刪除專案中的資料庫檔案 `lancedb/`、`valuecell.db`、`.knowledgebase/` 後重新啟動。
+若長時間未有更新，可以刪除本地資料並重新啟動：
+- LanceDB 目錄（位於系統應用程式目錄，與 `.env` 同路徑）：
+  - macOS: `~/Library/Application Support/ValueCell/lancedb`
+  - Linux: `~/.config/valuecell/lancedb`
+  - Windows: `%APPDATA%\\ValueCell\\lancedb`
+- 知識目錄（位於系統應用程式目錄，與 `.env` 同路徑）：
+  - macOS: `~/Library/Application Support/ValueCell/.knowledge`
+  - Linux: `~/.config/valuecell/.knowledge`
+  - Windows: `%APPDATA%\\ValueCell\\.knowledge`
+- SQLite 資料庫檔案（位於系統應用程式目錄，與 `.env` 同路徑）：
+  - macOS: `~/Library/Application Support/ValueCell/valuecell.db`
+  - Linux: `~/.config/valuecell/valuecell.db`
+  - Windows: `%APPDATA%\\ValueCell\\valuecell.db`
 
 
 # 開發者
diff --git a/docs/CONFIGURATION_GUIDE.md b/docs/CONFIGURATION_GUIDE.md
index 321d943d8..fdb0b6e51 100644
--- a/docs/CONFIGURATION_GUIDE.md
+++ b/docs/CONFIGURATION_GUIDE.md
@@ -58,10 +58,19 @@ bash start.sh
 
 The system will auto-detect available providers based on configured API keys.
 
-> **Note**: If you get database compatibility errors, delete these directories:
-> - `lancedb/`
-> - `valuecell.db`
-> - `.knowledgebase`
+> **Note**: If you get database compatibility errors, delete these locations:
+> - LanceDB directory (system application directory, same as `.env`):
+>   - macOS: `~/Library/Application Support/ValueCell/lancedb`
+>   - Linux: `~/.config/valuecell/lancedb`
+>   - Windows: `%APPDATA%\\ValueCell\\lancedb`
+> - Knowledge directory (system application directory, same as `.env`):
+>   - macOS: `~/Library/Application Support/ValueCell/.knowledge`
+>   - Linux: `~/.config/valuecell/.knowledge`
+>   - Windows: `%APPDATA%\\ValueCell\\.knowledge`
+> - SQLite database file (system application directory, same as `.env`):
+>   - macOS: `~/Library/Application Support/ValueCell/valuecell.db`
+>   - Linux: `~/.config/valuecell/valuecell.db`
+>   - Windows: `%APPDATA%\\ValueCell\\valuecell.db`
 
 ---
 
diff --git a/python/valuecell/core/coordinate/tests/test_e2e_persistence.py b/python/valuecell/core/coordinate/tests/test_e2e_persistence.py
index 231a93056..6ecc5e8a9 100644
--- a/python/valuecell/core/coordinate/tests/test_e2e_persistence.py
+++ b/python/valuecell/core/coordinate/tests/test_e2e_persistence.py
@@ -11,7 +11,8 @@
 @pytest.mark.asyncio
 async def test_orchestrator_buffer_store_e2e(tmp_path, monkeypatch):
     db_path = tmp_path / "e2e_valuecell.db"
-    monkeypatch.setenv("VALUECELL_SQLITE_DB", str(db_path))
+    # Use DATABASE_URL for tests; utils resolve_db_path will honor sqlite DSN
+    monkeypatch.setenv("VALUECELL_DATABASE_URL", f"sqlite:///{db_path}")
 
     monkeypatch.setattr(
         factory_mod, "create_model", lambda *args, **kwargs: "stub-model"
diff --git a/python/valuecell/server/config/settings.py b/python/valuecell/server/config/settings.py
index 2e4805c89..74d1aa0b1 100644
--- a/python/valuecell/server/config/settings.py
+++ b/python/valuecell/server/config/settings.py
@@ -4,6 +4,8 @@
 from functools import lru_cache
 from pathlib import Path
 
+from valuecell.utils.env import get_system_env_dir
+
 
 def _get_project_root() -> str:
     """Get project root directory path.
@@ -17,9 +19,15 @@ def _get_project_root() -> str:
 
 
 def _default_db_path() -> str:
-    """Get default database path in project root."""
-    repo_root = _get_project_root()
-    return f"sqlite:///{os.path.join(repo_root, 'valuecell.db')}"
+    """Get default database DSN under the system application directory.
+
+    Mirrors `.env` location so the SQLite file lives alongside user-level config:
+    - macOS: `~/Library/Application Support/ValueCell/valuecell.db`
+    - Linux: `~/.config/valuecell/valuecell.db`
+    - Windows: `%APPDATA%\ValueCell\valuecell.db`
+    """
+    system_dir = get_system_env_dir()
+    return f"sqlite:///{os.path.join(str(system_dir), 'valuecell.db')}"
 
 
 class Settings:
@@ -42,7 +50,13 @@ def __init__(self):
         self.CORS_ORIGINS = cors_origins.split(",") if cors_origins != "*" else ["*"]
 
         # Database Configuration
-        self.DATABASE_URL = os.getenv("VALUECELL_SQLITE_DB", _default_db_path())
+        # Prefer `VALUECELL_DATABASE_URL` if provided; otherwise use system application directory default.
+        env_db = os.getenv("VALUECELL_DATABASE_URL")
+        if env_db:
+            # If it's already a full DSN (sqlite or other), use as-is
+            self.DATABASE_URL = env_db
+        else:
+            self.DATABASE_URL = _default_db_path()
 
         # File Paths
         self.BASE_DIR = Path(__file__).parent.parent.parent
diff --git a/python/valuecell/server/db/README.md b/python/valuecell/server/db/README.md
index 526609a6a..db280c61f 100644
--- a/python/valuecell/server/db/README.md
+++ b/python/valuecell/server/db/README.md
@@ -21,8 +21,11 @@ db/
 
 Database configuration is defined in `valuecell/server/config/settings.py`:
 
-- **DATABASE_URL**: Database connection URL, defaults to `sqlite:///./valuecell.db`
-- **DB_ECHO**: Whether to output SQL logs, defaults to `false`
+- `VALUECELL_DATABASE_URL`: Database connection URL. Defaults to a SQLite file under the system application directory (same place as `.env`):
+  - macOS: `sqlite:///~/Library/Application Support/ValueCell/valuecell.db`
+  - Linux: `sqlite:///~/.config/valuecell/valuecell.db`
+  - Windows: `sqlite:///%APPDATA%/ValueCell/valuecell.db`
+- `DB_ECHO`: Whether to output SQL logs, defaults to `false`
 
 ## Database Models
 
@@ -224,7 +227,7 @@ else:
 1. **Password Security**: Default admin user password is a placeholder and should be replaced with proper hashed password in production environment
 2. **Database Backup**: SQLite database file should be backed up regularly
 3. **Permission Management**: Ensure database file has appropriate filesystem permissions
-4. **Environment Variables**: Database connection can be customized through `DATABASE_URL` environment variable
+4. **Environment Variables**: Database connection can be customized through `VALUECELL_DATABASE_URL` environment variable
 
 ## Troubleshooting
 
@@ -239,8 +242,13 @@ else:
 If you need to completely reset the database:
 
 ```bash
-# Delete existing database file
-rm valuecell.db
+# Delete existing database file (choose your OS path)
+# macOS
+rm -f "$HOME/Library/Application Support/ValueCell/valuecell.db"
+# Linux
+rm -f "$HOME/.config/valuecell/valuecell.db"
+# Windows (PowerShell)
+Remove-Item "$env:APPDATA\ValueCell\valuecell.db" -ErrorAction SilentlyContinue
 
 # Re-initialize
 python3 -m valuecell.server.db.init_db
diff --git a/python/valuecell/server/db/init_db.py b/python/valuecell/server/db/init_db.py
index b0a9f9f95..28e3a9c3b 100644
--- a/python/valuecell/server/db/init_db.py
+++ b/python/valuecell/server/db/init_db.py
@@ -2,6 +2,7 @@
 
 import json
 import logging
+import shutil
 import sys
 from pathlib import Path
 from typing import Optional
@@ -112,9 +113,25 @@ def create_database_file(self) -> bool:
                 # Create parent directories if they don't exist
                 db_path.parent.mkdir(parents=True, exist_ok=True)
 
-                # Create empty database file
-                db_path.touch()
-                logger.info(f"Created database file: {db_path}")
+                # If old repo-root DB exists and new system-path DB is missing, migrate it
+                try:
+                    repo_root = (
+                        Path(__file__).resolve().parent.parent.parent.parent.parent
+                    )
+                    old_repo_db = repo_root / "valuecell.db"
+                except Exception:
+                    old_repo_db = None
+
+                if old_repo_db and old_repo_db.exists() and not db_path.exists():
+                    shutil.copy2(old_repo_db, db_path)
+                    logger.info(
+                        f"Migrated existing database file from repo root to system directory: {db_path}"
+                    )
+
+                # Ensure database file exists
+                if not db_path.exists():
+                    db_path.touch()
+                    logger.info(f"Created database file: {db_path}")
                 return True
 
             except Exception as e:
diff --git a/python/valuecell/utils/db.py b/python/valuecell/utils/db.py
index 16c2138e9..edba1be81 100644
--- a/python/valuecell/utils/db.py
+++ b/python/valuecell/utils/db.py
@@ -1,15 +1,68 @@
 import os
+import shutil
+from pathlib import Path
 
+from .env import get_system_env_dir
 from .path import get_repo_root_path
 
 
+def _strip_sqlite_prefix(url_or_path: str) -> str:
+    """Normalize a potential SQLite DSN to a filesystem path.
+
+    - If `url_or_path` starts with `sqlite:///`, return the stripped path portion.
+    - Otherwise, return it unchanged.
+    """
+    if url_or_path.startswith("sqlite:///"):
+        return url_or_path.replace("sqlite:///", "", 1)
+    return url_or_path
+
+
 def resolve_db_path() -> str:
-    return os.environ.get("VALUECELL_SQLITE_DB") or os.path.join(
-        get_repo_root_path(), "valuecell.db"
-    )
+    """Resolve the SQLite database file path used by conversation stores.
+
+    Resolution order:
+    1) `DATABASE_URL` env var (if starts with `sqlite:///`, strip to path; otherwise ignore)
+    2) Default to system application directory (e.g., `~/Library/Application Support/ValueCell/valuecell.db` on macOS)
+
+    Note: This function returns a filesystem path, not a SQLAlchemy DSN.
+    """
+    # Prefer generic VALUECELL_DATABASE_URL if it points to SQLite
+    db_url = os.environ.get("VALUECELL_DATABASE_URL")
+    if db_url and db_url.startswith("sqlite:///"):
+        return _strip_sqlite_prefix(db_url)
+
+    # Default: store under system application directory alongside `.env`
+    return os.path.join(get_system_env_dir(), "valuecell.db")
 
 
 def resolve_lancedb_uri() -> str:
-    return os.environ.get("VALUECELL_LANCEDB_URI") or os.path.join(
-        get_repo_root_path(), "lancedb"
-    )
+    """Resolve LanceDB directory path.
+
+    Resolution order:
+    1) Default to system application directory: `<system_env_dir>/lancedb`
+
+    Additionally, if an old repo-root `lancedb` directory exists and the new
+    system directory does not, migrate the contents once for continuity.
+    """
+    # Default: system directory
+    system_dir = get_system_env_dir()
+    new_path = Path(system_dir) / "lancedb"
+    new_path.mkdir(parents=True, exist_ok=True)
+
+    # Migrate from old repo-root location if needed
+    old_path = Path(get_repo_root_path()) / "lancedb"
+    try:
+        if old_path.exists() and not any(new_path.iterdir()):
+            # Copy contents only if destination is empty
+            for item in old_path.iterdir():
+                src = item
+                dst = new_path / item.name
+                if item.is_dir():
+                    shutil.copytree(src, dst, dirs_exist_ok=True)
+                else:
+                    shutil.copy2(src, dst)
+    except Exception:
+        # Non-fatal: if migration fails, just proceed with new_path
+        pass
+
+    return str(new_path)
diff --git a/python/valuecell/utils/path.py b/python/valuecell/utils/path.py
index 61d2da619..26a6cb045 100644
--- a/python/valuecell/utils/path.py
+++ b/python/valuecell/utils/path.py
@@ -1,6 +1,16 @@
+"""Utilities for resolving Python package and repository root paths.
+
+Note: Database default location logic moved to `valuecell.utils.db.resolve_db_path`,
+which defaults to storing `valuecell.db` in the system application directory
+(same path as `.env`).
+"""
+
 import os
+import shutil
 from pathlib import Path
 
+from .env import get_system_env_dir
+
 
 def get_python_root_path() -> str:
     """
@@ -28,10 +38,11 @@ def get_python_root_path() -> str:
 
 
 def get_repo_root_path() -> str:
-    """Resolve repository root and return default DB path valuecell.db.
+    """
+    Resolve repository root directory path.
 
-    Layout assumption: this file is at repo_root/python/valuecell/utils/db.py
-    We walk up 3 levels to reach repo_root.
+    Assumes this file is at `repo_root/python/valuecell/utils/path.py`.
+    Walk up three levels to reach `repo_root`.
     """
     here = os.path.dirname(__file__)
     repo_root = os.path.abspath(os.path.join(here, "..", "..", ".."))
@@ -52,11 +63,28 @@ def get_agent_card_path() -> str:
 
 def get_knowledge_path() -> str:
     """
-    Returns the path to the knowledge directory located in the project root.
+    Resolve the Knowledge directory path under the system application directory.
 
-    Returns:
-        str: Absolute path of the knowledge directory
+    Behavior:
+    - Default location: `<system_env_dir>/.knowledge` (same base dir as `.env`)
+    - One-time migration: if old repo-root `.knowledge` exists and the system dir
+      is empty, copy the contents for continuity.
     """
-    root_path = get_repo_root_path()
-    knowledge_path = Path(root_path) / ".knowledge"
-    return str(knowledge_path)
+    new_path = Path(get_system_env_dir()) / ".knowledge"
+    new_path.mkdir(parents=True, exist_ok=True)
+
+    old_path = Path(get_repo_root_path()) / ".knowledge"
+    try:
+        if old_path.exists() and not any(new_path.iterdir()):
+            for item in old_path.iterdir():
+                src = item
+                dst = new_path / item.name
+                if item.is_dir():
+                    shutil.copytree(src, dst, dirs_exist_ok=True)
+                else:
+                    shutil.copy2(src, dst)
+    except Exception:
+        # Non-fatal: proceed with new_path even if migration fails
+        pass
+
+    return str(new_path)