diff --git a/pkg/config/file_source.go b/pkg/config/file_source.go
index 4eace878d890f..535e87d5c2963 100644
--- a/pkg/config/file_source.go
+++ b/pkg/config/file_source.go
@@ -19,6 +19,7 @@ package config
 import (
 	"bytes"
 	"fmt"
+	"io"
 	"os"
 	"path/filepath"
 	"sync"
@@ -146,7 +147,7 @@ func (fs *FileSource) loadFromFile() error {
 
 		var node yaml.Node
 		decoder := yaml.NewDecoder(bytes.NewReader(data))
-		if err := decoder.Decode(&node); err != nil {
+		if err := decoder.Decode(&node); err != nil && !errors.Is(err, io.EOF) {
 			return errors.Wrap(err, "YAML unmarshal failed: "+configFile)
 		}
 
diff --git a/pkg/config/file_source_test.go b/pkg/config/file_source_test.go
new file mode 100644
index 0000000000000..60abdb110ed7d
--- /dev/null
+++ b/pkg/config/file_source_test.go
@@ -0,0 +1,32 @@
+package config
+
+import (
+	"os"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+func TestEmptyYaml(t *testing.T) {
+	file, err := os.CreateTemp(os.TempDir(), "milvus_ut_config_fs_*.yaml")
+	require.NoError(t, err)
+
+	filepath := file.Name()
+
+	file.WriteString("#")
+	file.Close()
+
+	defer os.Remove(filepath)
+
+	fs := NewFileSource(&FileInfo{
+		Files:           []string{filepath},
+		RefreshInterval: time.Hour,
+	})
+
+	_, err = fs.GetConfigurations()
+	assert.NoError(t, err)
+
+	fs.Close()
+}