diff --git a/pkg/api/kpm_run.go b/pkg/api/kpm_run.go
index 80612cb5..9f1a521f 100644
--- a/pkg/api/kpm_run.go
+++ b/pkg/api/kpm_run.go
@@ -69,6 +69,10 @@ func RunPkgInPath(opts *opt.CompileOptions) (string, error) {
 // CompileWithOpt will compile the kcl program without kcl package.
 // Deprecated: This method will not be maintained in the future. Use RunWithOpts instead.
 func RunWithOpt(opts *opt.CompileOptions) (*kcl.KCLResultList, error) {
+	// The entries will override the entries in the settings file.
+	if opts.HasSettingsYaml() && len(opts.KFilenameList) > 0 && len(opts.Entries()) > 0 {
+		opts.KFilenameList = []string{}
+	}
 	if len(opts.Entries()) > 0 {
 		for _, entry := range opts.Entries() {
 			if filepath.IsAbs(entry) {
diff --git a/pkg/api/kpm_run_test.go b/pkg/api/kpm_run_test.go
index 0597c2ae..46b17718 100644
--- a/pkg/api/kpm_run_test.go
+++ b/pkg/api/kpm_run_test.go
@@ -131,6 +131,16 @@ func TestRunWithSettingsOpts(t *testing.T) {
 	assert.Equal(t, err, nil)
 }
 
+func TestRunWithSettingsOptsAndFile(t *testing.T) {
+	pkgPath := getTestDir("test_settings")
+	opts := opt.DefaultCompileOptions()
+	opts.Merge(kcl.WithSettings(filepath.Join(pkgPath, "kcl.yaml")))
+	opts.SetHasSettingsYaml(true)
+	opts.SetEntries([]string{filepath.Join(pkgPath, "test.k")})
+	_, err := RunWithOpt(opts)
+	assert.Equal(t, err, nil)
+}
+
 func TestRunTarPkg(t *testing.T) {
 	pkgPath := getTestDir("test_run_tar_in_path")
 	tarPath, _ := filepath.Abs(filepath.Join(pkgPath, "test.tar"))