diff --git a/pkg/filesystem/fs.go b/pkg/filesystem/fs.go
index b7e68e1c02..118f97c9c9 100644
--- a/pkg/filesystem/fs.go
+++ b/pkg/filesystem/fs.go
@@ -55,7 +55,7 @@ type Filesystem struct {
 	rootMountpoint       string
 }
 
-func (fs *Filesystem) tryRetainSharedDaemon(d *daemon.Daemon) {
+func (fs *Filesystem) TryRetainSharedDaemon(d *daemon.Daemon) {
 	// FsDriver can be changed between two startups.
 	if d.HostMountpoint() == fs.rootMountpoint || config.GetFsDriver() == config.FsDriverFscache {
 		fs.sharedDaemon = d
@@ -110,13 +110,13 @@ func NewFileSystem(ctx context.Context, opt ...NewFSOpt) (*Filesystem, error) {
 
 		// Found shared daemon
 		// Fscache userspace daemon has no host mountpoint.
-		fs.tryRetainSharedDaemon(d)
+		fs.TryRetainSharedDaemon(d)
 
 	}
 
 	for _, d := range liveDaemons {
 		// Found shared daemon
-		fs.tryRetainSharedDaemon(d)
+		fs.TryRetainSharedDaemon(d)
 	}
 
 	return &fs, nil
diff --git a/pkg/system/system.go b/pkg/system/system.go
index f1d7c3ae1e..7a7250e29a 100644
--- a/pkg/system/system.go
+++ b/pkg/system/system.go
@@ -25,6 +25,7 @@ import (
 	"github.com/containerd/nydus-snapshotter/pkg/daemon"
 	"github.com/containerd/nydus-snapshotter/pkg/daemon/types"
 	"github.com/containerd/nydus-snapshotter/pkg/errdefs"
+	"github.com/containerd/nydus-snapshotter/pkg/filesystem"
 	"github.com/containerd/nydus-snapshotter/pkg/manager"
 	metrics "github.com/containerd/nydus-snapshotter/pkg/metrics/tool"
 )
@@ -50,6 +51,7 @@ const defaultErrorCode string = "Unknown"
 // 3. Rolling update
 // 4. Daemons failures record as metrics
 type Controller struct {
+	fs      *filesystem.Filesystem
 	manager *manager.Manager
 	// httpSever *http.Server
 	addr   *net.UnixAddr
@@ -117,7 +119,7 @@ type rafsInstanceInfo struct {
 	ImageID     string `json:"image_id"`
 }
 
-func NewSystemController(manager *manager.Manager, sock string) (*Controller, error) {
+func NewSystemController(fs *filesystem.Filesystem, manager *manager.Manager, sock string) (*Controller, error) {
 	if err := os.MkdirAll(filepath.Dir(sock), os.ModePerm); err != nil {
 		return nil, err
 	}
@@ -134,6 +136,7 @@ func NewSystemController(manager *manager.Manager, sock string) (*Controller, er
 	}
 
 	sc := Controller{
+		fs:      fs,
 		manager: manager,
 		addr:    addr,
 		router:  mux.NewRouter(),
@@ -293,6 +296,7 @@ func (sc *Controller) upgradeNydusDaemon(d *daemon.Daemon, c upgradeRequest) err
 	log.L.Infof("Upgrading nydusd %s, request %v", d.ID(), c)
 
 	manager := sc.manager
+	fs := sc.fs
 
 	var new daemon.Daemon
 	new.States = d.States
@@ -337,6 +341,8 @@ func (sc *Controller) upgradeNydusDaemon(d *daemon.Daemon, c upgradeRequest) err
 		return errors.Wrap(err, "old daemon exits")
 	}
 
+	fs.TryRetainSharedDaemon(&new)
+
 	if err := new.Start(); err != nil {
 		return errors.Wrap(err, "start file system service")
 	}
diff --git a/snapshot/snapshot.go b/snapshot/snapshot.go
index 488ca6d68d..d7545835f1 100644
--- a/snapshot/snapshot.go
+++ b/snapshot/snapshot.go
@@ -39,10 +39,10 @@ import (
 	"github.com/containerd/nydus-snapshotter/pkg/metrics"
 	"github.com/containerd/nydus-snapshotter/pkg/metrics/collector"
 	"github.com/containerd/nydus-snapshotter/pkg/pprof"
+	"github.com/containerd/nydus-snapshotter/pkg/system"
 
 	"github.com/containerd/nydus-snapshotter/pkg/resolve"
 	"github.com/containerd/nydus-snapshotter/pkg/store"
-	"github.com/containerd/nydus-snapshotter/pkg/system"
 
 	"github.com/containerd/nydus-snapshotter/pkg/filesystem"
 	"github.com/containerd/nydus-snapshotter/pkg/label"
@@ -122,24 +122,6 @@ func NewSnapshotter(ctx context.Context, cfg *config.SnapshotterConfig) (snapsho
 		}()
 	}
 
-	if config.IsSystemControllerEnabled() {
-		systemController, err := system.NewSystemController(manager, config.SystemControllerAddress())
-		if err != nil {
-			return nil, errors.Wrap(err, "create system controller")
-		}
-		go func() {
-			if err := systemController.Run(); err != nil {
-				log.L.WithError(err).Error("Failed to start system controller")
-			}
-		}()
-		pprofAddress := config.SystemControllerPprofAddress()
-		if pprofAddress != "" {
-			if err := pprof.NewPprofHTTPListener(pprofAddress); err != nil {
-				return nil, errors.Wrap(err, "Failed to start pprof HTTP server")
-			}
-		}
-	}
-
 	opts := []filesystem.NewFSOpt{
 		filesystem.WithManager(manager),
 		filesystem.WithNydusImageBinaryPath(cfg.DaemonConfig.NydusdPath),
@@ -169,6 +151,24 @@ func NewSnapshotter(ctx context.Context, cfg *config.SnapshotterConfig) (snapsho
 		return nil, errors.Wrap(err, "failed to initialize nydus filesystem")
 	}
 
+	if config.IsSystemControllerEnabled() {
+		systemController, err := system.NewSystemController(nydusFs, manager, config.SystemControllerAddress())
+		if err != nil {
+			return nil, errors.Wrap(err, "create system controller")
+		}
+		go func() {
+			if err := systemController.Run(); err != nil {
+				log.L.WithError(err).Error("Failed to start system controller")
+			}
+		}()
+		pprofAddress := config.SystemControllerPprofAddress()
+		if pprofAddress != "" {
+			if err := pprof.NewPprofHTTPListener(pprofAddress); err != nil {
+				return nil, errors.Wrap(err, "Failed to start pprof HTTP server")
+			}
+		}
+	}
+
 	// With fuse driver enabled and a fuse daemon configuration with "localfs"
 	// storage backend, it indicates that a Blobs Manager is needed to download
 	// blobs from registry alone with no help of nydusd or containerd.