diff --git a/cmd/kcl/commands/run.go b/cmd/kcl/commands/run.go
index f3cb698..d4ca580 100644
--- a/cmd/kcl/commands/run.go
+++ b/cmd/kcl/commands/run.go
@@ -27,20 +27,32 @@ For example, 'kcl run path/to/kcl.k' will run the file named path/to/kcl.k
   # Run multiple files
   kcl run path/to/kcl1.k path/to/kcl2.k
 
-  # Run OCI packages
+  # Run OCI modules
   kcl run oci://ghcr.io/kcl-lang/helloworld --tag 0.1.0
 
   # Run remote Git repo
   kcl run git://github.com/kcl-lang/flask-demo-kcl-manifests --commit ade147b
 
-  # Run OCI packages by flag
+  # Run OCI modules by flag
   kcl run --oci https://ghcr.io/kcl-lang/helloworld --tag 0.1.0
 
   # Run remote module from Git with branch repo by flag
   kcl run --git https://github.com/kcl-lang/flask-demo-kcl-manifests --branch main
 
   # Run remote module from Git with branch repo by flag with ssh url
-  kcl run --git ssh://github.com/kcl-lang/flask-demo-kcl-manifests --branch main`
+  kcl run --git ssh://github.com/kcl-lang/flask-demo-kcl-manifests --branch main
+ 
+  # Run OCI submodule by flag
+  kcl run subhelloworld --oci https://ghcr.io/kcl-lang/helloworld --tag 0.1.4
+
+  # Run OCI submodule with version by flag
+  kcl run subhelloworld:0.0.1 --oci https://ghcr.io/kcl-lang/helloworld --tag 0.1.4
+
+  # Run Git submodule by flag
+  kcl run cc --git https://github.com/kcl-lang/flask-demo-kcl-manifests --commit 8308200
+
+  # Run Git submodule by flag
+  kcl run cc:0.0.1 --git https://github.com/kcl-lang/flask-demo-kcl-manifests --commit 8308200`
 )
 
 // NewRunCmd returns the run command.
diff --git a/pkg/options/run.go b/pkg/options/run.go
index ea47b28..b5f9138 100644
--- a/pkg/options/run.go
+++ b/pkg/options/run.go
@@ -20,9 +20,11 @@ import (
 	"kcl-lang.io/kcl-go/pkg/tools/gen"
 	"kcl-lang.io/kpm/pkg/client"
 	"kcl-lang.io/kpm/pkg/constants"
+	"kcl-lang.io/kpm/pkg/downloader"
 	"kcl-lang.io/kpm/pkg/opt"
 	pkg "kcl-lang.io/kpm/pkg/package"
 	"kcl-lang.io/kpm/pkg/runner"
+	"kcl-lang.io/kpm/pkg/utils"
 )
 
 const (
@@ -79,6 +81,8 @@ type RunOptions struct {
 	Format string
 	// Writer is used to output the run result. Default is os.Stdout.
 	Writer io.Writer
+	// ModSpec is the module spec for the KCL module.
+	ModSpec *downloader.ModSpec
 }
 
 // NewRunOptions returns a new instance of RunOptions with default values.
@@ -125,7 +129,8 @@ func (o *RunOptions) Run() error {
 			o.Entries[i] = entry
 		}
 	}
-	result, err = cli.Run(
+
+	opts := []client.RunOption{
 		client.WithRunSourceUrls(o.Entries),
 		client.WithSettingFiles(o.Settings),
 		client.WithArguments(o.Arguments),
@@ -140,7 +145,13 @@ func (o *RunOptions) Run() error {
 		client.WithStrictRange(o.StrictRangeCheck),
 		client.WithCompileOnly(o.CompileOnly),
 		client.WithLogger(os.Stdout),
-	)
+	}
+
+	if o.ModSpec != nil {
+		opts = append(opts, client.WithRunModSpec(o.ModSpec))
+	}
+
+	result, err = cli.Run(opts...)
 
 	if err != nil {
 		if o.NoStyle {
@@ -196,22 +207,30 @@ func (o *RunOptions) Complete(args []string) error {
 	}
 
 	for _, arg := range args {
-		argUrl, err := url.Parse(arg)
-		if err != nil {
-			return err
-		}
-		query := argUrl.Query()
-		if o.Tag != "" {
-			query.Set("tag", o.Tag)
-		}
-		if o.Commit != "" {
-			query.Set("commit", o.Commit)
-		}
-		if o.Branch != "" {
-			query.Set("branch", o.Branch)
+
+		modSpec := downloader.ModSpec{}
+		err := modSpec.FromString(arg)
+		// If the arg is a directory or is not a Mod Spec, parse it as other source
+		if utils.DirExists(arg) || err != nil {
+			argUrl, err := url.Parse(arg)
+			if err != nil {
+				return err
+			}
+			query := argUrl.Query()
+			if o.Tag != "" {
+				query.Set("tag", o.Tag)
+			}
+			if o.Commit != "" {
+				query.Set("commit", o.Commit)
+			}
+			if o.Branch != "" {
+				query.Set("branch", o.Branch)
+			}
+			argUrl.RawQuery = query.Encode()
+			o.Entries = append(o.Entries, argUrl.String())
+		} else {
+			o.ModSpec = &modSpec
 		}
-		argUrl.RawQuery = query.Encode()
-		o.Entries = append(o.Entries, argUrl.String())
 	}
 	return nil
 }
diff --git a/pkg/options/run_test.go b/pkg/options/run_test.go
index 2028ab4..d83e6d4 100644
--- a/pkg/options/run_test.go
+++ b/pkg/options/run_test.go
@@ -108,14 +108,14 @@ spec:
 
 func TestRunOptions_Complete(t *testing.T) {
 	options := NewRunOptions()
-	args := []string{"file1.k", "file2.k", "file3.k"}
+	args := []string{"./testdata/run_opt/file1.k", "./testdata/run_opt/file2.k", "./testdata/run_opt/file3.k"}
 
 	err := options.Complete(args)
 	if err != nil {
 		t.Errorf("RunOptions.Complete() failed: %v", err)
 	}
 
-	expectedEntries := []string{"file1.k", "file2.k", "file3.k"}
+	expectedEntries := []string{"./testdata/run_opt/file1.k", "./testdata/run_opt/file2.k", "./testdata/run_opt/file3.k"}
 
 	if len(options.Entries) != len(expectedEntries) {
 		t.Fatalf("unexpected number of entries:\nexpected: %d\ngot: %d", len(expectedEntries), len(options.Entries))
diff --git a/pkg/options/testdata/run_opt/file1.k b/pkg/options/testdata/run_opt/file1.k
new file mode 100644
index 0000000..e03bc79
--- /dev/null
+++ b/pkg/options/testdata/run_opt/file1.k
@@ -0,0 +1 @@
+file1 = 1
\ No newline at end of file
diff --git a/pkg/options/testdata/run_opt/file2.k b/pkg/options/testdata/run_opt/file2.k
new file mode 100644
index 0000000..da1d487
--- /dev/null
+++ b/pkg/options/testdata/run_opt/file2.k
@@ -0,0 +1 @@
+file2 = 2
\ No newline at end of file
diff --git a/pkg/options/testdata/run_opt/file3.k b/pkg/options/testdata/run_opt/file3.k
new file mode 100644
index 0000000..2ab07ef
--- /dev/null
+++ b/pkg/options/testdata/run_opt/file3.k
@@ -0,0 +1 @@
+file3 = 3
\ No newline at end of file
diff --git a/test/e2e/test_suites/test_kcl_run_29/input b/test/e2e/test_suites/test_kcl_run_29/input
new file mode 100644
index 0000000..2172a4e
--- /dev/null
+++ b/test/e2e/test_suites/test_kcl_run_29/input
@@ -0,0 +1 @@
+kcl run subhelloworld --oci https://ghcr.io/kcl-lang/helloworld --tag 0.1.4
\ No newline at end of file
diff --git a/test/e2e/test_suites/test_kcl_run_29/stderr b/test/e2e/test_suites/test_kcl_run_29/stderr
new file mode 100644
index 0000000..e69de29
diff --git a/test/e2e/test_suites/test_kcl_run_29/stdout b/test/e2e/test_suites/test_kcl_run_29/stdout
new file mode 100644
index 0000000..9df0d7c
--- /dev/null
+++ b/test/e2e/test_suites/test_kcl_run_29/stdout
@@ -0,0 +1 @@
+The_first_sub_kcl_program: Hello Sub World!
\ No newline at end of file
diff --git a/test/e2e/test_suites/test_kcl_run_30/input b/test/e2e/test_suites/test_kcl_run_30/input
new file mode 100644
index 0000000..7a790ba
--- /dev/null
+++ b/test/e2e/test_suites/test_kcl_run_30/input
@@ -0,0 +1 @@
+kcl run subhelloworld:0.0.1 --oci https://ghcr.io/kcl-lang/helloworld --tag 0.1.4
\ No newline at end of file
diff --git a/test/e2e/test_suites/test_kcl_run_30/stderr b/test/e2e/test_suites/test_kcl_run_30/stderr
new file mode 100644
index 0000000..e69de29
diff --git a/test/e2e/test_suites/test_kcl_run_30/stdout b/test/e2e/test_suites/test_kcl_run_30/stdout
new file mode 100644
index 0000000..9df0d7c
--- /dev/null
+++ b/test/e2e/test_suites/test_kcl_run_30/stdout
@@ -0,0 +1 @@
+The_first_sub_kcl_program: Hello Sub World!
\ No newline at end of file
diff --git a/test/e2e/test_suites/test_kcl_run_31/input b/test/e2e/test_suites/test_kcl_run_31/input
new file mode 100644
index 0000000..0e25c32
--- /dev/null
+++ b/test/e2e/test_suites/test_kcl_run_31/input
@@ -0,0 +1 @@
+kcl run cc --git https://github.com/kcl-lang/flask-demo-kcl-manifests --commit 8308200
\ No newline at end of file
diff --git a/test/e2e/test_suites/test_kcl_run_31/stderr b/test/e2e/test_suites/test_kcl_run_31/stderr
new file mode 100644
index 0000000..e69de29
diff --git a/test/e2e/test_suites/test_kcl_run_31/stdout b/test/e2e/test_suites/test_kcl_run_31/stdout
new file mode 100644
index 0000000..f405925
--- /dev/null
+++ b/test/e2e/test_suites/test_kcl_run_31/stdout
@@ -0,0 +1 @@
+The_first_kcl_program: Hello World!
\ No newline at end of file
diff --git a/test/e2e/test_suites/test_kcl_run_32/input b/test/e2e/test_suites/test_kcl_run_32/input
new file mode 100644
index 0000000..496d0a1
--- /dev/null
+++ b/test/e2e/test_suites/test_kcl_run_32/input
@@ -0,0 +1 @@
+kcl run cc:0.0.1 --git https://github.com/kcl-lang/flask-demo-kcl-manifests --commit 8308200
\ No newline at end of file
diff --git a/test/e2e/test_suites/test_kcl_run_32/stderr b/test/e2e/test_suites/test_kcl_run_32/stderr
new file mode 100644
index 0000000..e69de29
diff --git a/test/e2e/test_suites/test_kcl_run_32/stdout b/test/e2e/test_suites/test_kcl_run_32/stdout
new file mode 100644
index 0000000..d2dcf2a
--- /dev/null
+++ b/test/e2e/test_suites/test_kcl_run_32/stdout
@@ -0,0 +1 @@
+The_first_kcl_program: Hello World!