diff --git a/internal/app/skill_setup.go b/internal/app/skill_setup.go
index 6c0becf4..2d2abf24 100644
--- a/internal/app/skill_setup.go
+++ b/internal/app/skill_setup.go
@@ -127,7 +127,7 @@ var (
 	skillSetupExecutable      = os.Executable
 	skillSetupGetwd           = os.Getwd
 	skillSetupUserHomeDir     = os.UserHomeDir
-	skillSetupSystemHomeDir   = os.UserHomeDir
+	skillSetupSystemHomeDir   = upgrade.ResolveSystemHomeDir
 	skillSetupRemoveAll       = os.RemoveAll
 	skillSetupBackupAndRemove = upgrade.BackupAndRemoveSkillDir
 	skillSetupRestoreBackup   = upgrade.RestoreSkillPath
diff --git a/internal/upgrade/paths.go b/internal/upgrade/paths.go
index f0424ae6..d0edb495 100644
--- a/internal/upgrade/paths.go
+++ b/internal/upgrade/paths.go
@@ -7,6 +7,7 @@ import (
 	"errors"
 	"fmt"
 	"os"
+	"os/user"
 	"path/filepath"
 	"runtime"
 	"sort"
@@ -139,9 +140,26 @@ var universalSkillDirs = map[string]bool{
 	".amp/skills":      true,
 }
 
+// upgradeCurrentUser is the test seam backing ResolveSystemHomeDir.
+var upgradeCurrentUser = user.Current
+
+// ResolveSystemHomeDir returns the operating-system user's real home directory
+// independent of the $HOME environment variable. $HOME may be overridden in
+// isolated or verifier contexts, so the app-bundle detection gate
+// (allowSystemApps = homeDir == systemHome) must compare against a HOME-
+// independent source to actually mean "operating on the real user profile".
+// It prefers the OS user database (getpwuid on Unix) and falls back to $HOME
+// only when the user record cannot be resolved.
+func ResolveSystemHomeDir() (string, error) {
+	if u, err := upgradeCurrentUser(); err == nil && u.HomeDir != "" {
+		return u.HomeDir, nil
+	}
+	return os.UserHomeDir()
+}
+
 var (
 	upgradeUserHomeDir     = os.UserHomeDir
-	upgradeSystemHomeDir   = os.UserHomeDir
+	upgradeSystemHomeDir   = ResolveSystemHomeDir
 	upgradeExecutable      = os.Executable
 	upgradeEvalSymlinks    = filepath.EvalSymlinks
 	upgradeCopyDir         = copyDir
diff --git a/internal/upgrade/system_home_test.go b/internal/upgrade/system_home_test.go
new file mode 100644
index 00000000..7870742f
--- /dev/null
+++ b/internal/upgrade/system_home_test.go
@@ -0,0 +1,49 @@
+package upgrade
+
+import (
+	"errors"
+	"os/user"
+	"testing"
+
+	"github.com/DingTalk-Real-AI/dingtalk-workspace-cli/internal/testseam"
+)
+
+// TestCrossPlatformCoverageSystemHomeIndependentOfHOME pins that the app-bundle
+// detection gate compares against a HOME-independent system home: ResolveSystemHomeDir
+// prefers the OS user record (getpwuid on Unix) and only falls back to $HOME when that
+// record cannot be resolved. Without this, allowSystemApps = homeDir == systemHome is a
+// no-op whenever $HOME is overridden, because both sides would honor the same override.
+func TestCrossPlatformCoverageSystemHomeIndependentOfHOME(t *testing.T) {
+	// Success path: the OS user database home is returned as-is.
+	testseam.Swap(t, &upgradeCurrentUser, func() (*user.User, error) {
+		return &user.User{HomeDir: "/tmp/dws-real-system-home"}, nil
+	})
+	got, err := ResolveSystemHomeDir()
+	if err != nil || got != "/tmp/dws-real-system-home" {
+		t.Fatalf("ResolveSystemHomeDir success = (%q, %v), want /tmp/dws-real-system-home", got, err)
+	}
+
+	// Fallback path: when the user record is unavailable, fall back to $HOME.
+	testseam.Swap(t, &upgradeCurrentUser, func() (*user.User, error) {
+		return nil, errors.New("user record unavailable")
+	})
+	got, err = ResolveSystemHomeDir()
+	if err != nil {
+		t.Fatalf("ResolveSystemHomeDir fallback returned error: %v", err)
+	}
+	if got == "" {
+		t.Fatalf("ResolveSystemHomeDir fallback returned empty home")
+	}
+
+	// Empty HomeDir is also treated as "unresolved" and falls back.
+	testseam.Swap(t, &upgradeCurrentUser, func() (*user.User, error) {
+		return &user.User{HomeDir: ""}, nil
+	})
+	got, err = ResolveSystemHomeDir()
+	if err != nil {
+		t.Fatalf("ResolveSystemHomeDir empty-home fallback returned error: %v", err)
+	}
+	if got == "" {
+		t.Fatalf("ResolveSystemHomeDir empty-home fallback returned empty home")
+	}
+}