diff --git a/pkg/client/client_test.go b/pkg/client/client_test.go
index 97799b9e..b47161f5 100644
--- a/pkg/client/client_test.go
+++ b/pkg/client/client_test.go
@@ -1850,6 +1850,45 @@ func TestRunLocalWithArgs(t *testing.T) {
 		}, []string{
 			filepath.Join(pkgPath, "with_args", "run_11", "sub", "kcl.yaml"),
 		}, filepath.Join(pkgPath, "with_args", "run_11"), false, "", "The_sub_kcl_program: Hello Sub World!"},
+		{
+			[]string{filepath.Join(pkgPath, "with_args", "run_0", "main.k")}, []string{}, filepath.Join(pkgPath, "with_args", "run_0"),
+			false, "", "The_first_kcl_program: Hello World!"},
+		{
+			[]string{filepath.Join(pkgPath, "with_args", "run_1", "main.k")}, []string{}, filepath.Join(pkgPath, "with_args", "run_1"),
+			false, "", "The_first_kcl_program: Hello World!"},
+		{[]string{
+			filepath.Join(pkgPath, "with_args", "run_2", "base.k"),
+			filepath.Join(pkgPath, "with_args", "run_2", "main.k"),
+		}, []string{}, "", false, "", "base: Base\nThe_first_kcl_program: Hello World!"},
+		{[]string{
+			filepath.Join(pkgPath, "with_args", "run_3", "main.k"),
+		}, []string{}, "", false, "", "The_first_kcl_program: Hello World!"},
+		{[]string{
+			filepath.Join(pkgPath, "with_args", "run_4", "main.k"),
+		}, []string{}, "", false, "", "The_first_kcl_program: Hello World!"},
+		{[]string{
+			filepath.Join(pkgPath, "with_args", "run_5"),
+		}, []string{}, "", false, "", "The_first_kcl_program: Hello World!"},
+		{[]string{
+			filepath.Join(pkgPath, "with_args", "run_6"),
+		}, []string{}, "", false, "", "The_first_kcl_program: Hello World!"},
+		{[]string{
+			filepath.Join(pkgPath, "with_args", "run_7"),
+		}, []string{}, "", false, "", "base: Base\nThe_first_kcl_program: Hello World!"},
+		{[]string{
+			filepath.Join(pkgPath, "with_args", "run_8"),
+		}, []string{}, "", false, "", "sub: SUB"},
+		{[]string{
+			filepath.Join(pkgPath, "with_args", "run_9"),
+		}, []string{}, "", false, "", "The_sub_kcl_program: Hello Sub World!"},
+		{[]string{}, []string{
+			filepath.Join(pkgPath, "with_args", "run_10", "sub", "kcl.yaml"),
+		}, "", false, "", "The_sub_kcl_program_1: Hello Sub World 1!"},
+		{[]string{
+			filepath.Join(pkgPath, "with_args", "run_11", "sub", "sub.k"),
+		}, []string{
+			filepath.Join(pkgPath, "with_args", "run_11", "sub", "kcl.yaml"),
+		}, "", false, "", "The_sub_kcl_program: Hello Sub World!"},
 	}
 
 	for _, test := range tests {
diff --git a/pkg/client/run.go b/pkg/client/run.go
index e52be324..dd480b7f 100644
--- a/pkg/client/run.go
+++ b/pkg/client/run.go
@@ -378,12 +378,31 @@ func getCompileOptionsFromKclMod(kclPkg *pkg.KclPkg) *kcl.Option {
 func (o *RunOptions) applyCompileOptions(source downloader.Source, kclPkg *pkg.KclPkg, workDir string) error {
 	o.Merge(kcl.WithWorkDir(workDir))
 
+	// Check if the source is a local path and is the kcl package.
+	sourceIsKclPackage := func(pkgSource *downloader.Source) bool {
+		if !pkgSource.IsLocalPath() {
+			return false
+		}
+		sourcePath := pkgSource.Path
+		if !filepath.IsAbs(sourcePath) && !utils.IsModRelativePath(sourcePath) {
+			sourcePath = filepath.Join(workDir, sourcePath)
+		}
+
+		pkgHome := kclPkg.HomePath
+
+		if !filepath.IsAbs(pkgHome) && !utils.IsModRelativePath(sourcePath) {
+			pkgHome = filepath.Join(workDir, pkgHome)
+		}
+
+		return sourcePath == pkgHome
+	}
+
 	// If the sources from cli is not empty, use the sources from cli.
 	if len(o.Sources) != 0 {
 		var compiledFiles []string
 		// All the cli relative path should be transformed to the absolute path by workdir
 		for _, source := range o.Sources {
-			if source.IsLocalPath() && source.Path != kclPkg.HomePath {
+			if source.IsLocalPath() && !sourceIsKclPackage(source) {
 				sPath := source.Path
 				if !filepath.IsAbs(sPath) && !utils.IsModRelativePath(sPath) {
 					sPath = filepath.Join(workDir, sPath)
@@ -402,7 +421,7 @@ func (o *RunOptions) applyCompileOptions(source downloader.Source, kclPkg *pkg.K
 	var yamlOpts *kcl.Option
 	// For the packaged kcl package, git, oci and tar, settings yaml file should be find from the package path if not set by cli.
 	// For the local kcl package, settings yaml file should be find from the workdir if not set by cli.
-	if source.IsPackaged() {
+	if source.IsPackaged() || sourceIsKclPackage(&source) {
 		yamlOpts = o.getCompileOptionsFromYaml(kclPkg.HomePath)
 	} else {
 		yamlOpts = o.getCompileOptionsFromYaml(workDir)
@@ -431,7 +450,7 @@ func (o *RunOptions) applyCompileOptions(source downloader.Source, kclPkg *pkg.K
 	if len(o.KFilenameList) == 0 {
 		// For the packaged kcl package, git, oci and tar, no *.k files are set by cli, kcl.yaml or kcl.mod, compile the package path.
 		// For the local kcl package, no *.k files are set by cli, kcl.yaml or kcl.mod, compile the workdir.
-		if source.IsPackaged() {
+		if source.IsPackaged() || sourceIsKclPackage(&source) {
 			o.KFilenameList = []string{kclPkg.HomePath}
 		} else {
 			o.KFilenameList = []string{workDir}