diff --git a/cmd/sealos/cmd/gen.go b/cmd/sealos/cmd/gen.go
index 786e27a1923..c0180330929 100644
--- a/cmd/sealos/cmd/gen.go
+++ b/cmd/sealos/cmd/gen.go
@@ -24,6 +24,7 @@ import (
 	"github.com/spf13/cobra"
 
 	"github.com/labring/sealos/pkg/apply"
+	"github.com/labring/sealos/pkg/utils/logger"
 )
 
 var exampleGen = `
@@ -65,6 +66,7 @@ func newGenCmd() *cobra.Command {
 			var outputWriter io.WriteCloser
 			switch out {
 			case "", "stdout":
+				logger.Info("if you want to save the output of gen command, use '--output' option instead of redirecting to file")
 				outputWriter = os.Stdout
 			default:
 				outputWriter, err = os.Create(out)
diff --git a/pkg/apply/args.go b/pkg/apply/args.go
index 31b98bf993e..d5ec84182a2 100644
--- a/pkg/apply/args.go
+++ b/pkg/apply/args.go
@@ -65,7 +65,7 @@ type RunArgs struct {
 func (arg *RunArgs) RegisterFlags(fs *pflag.FlagSet) {
 	arg.Cluster.RegisterFlags(fs, "run with", "run")
 	arg.SSH.RegisterFlags(fs)
-	fs.StringSliceVarP(&arg.CustomEnv, "env", "e", []string{}, "environment variables to set during command execution")
+	fs.StringSliceVarP(&arg.CustomEnv, "env", "e", []string{}, "environment variables to be set for images")
 	fs.StringSliceVar(&arg.CustomCMD, "cmd", []string{}, "override CMD directive in images")
 	fs.StringSliceVar(&arg.CustomConfigFiles, "config-file", []string{}, "path of custom config files, to use to replace the resource")
 }
@@ -80,7 +80,7 @@ type Args struct {
 func (arg *Args) RegisterFlags(fs *pflag.FlagSet) {
 	fs.StringSliceVar(&arg.Values, "values", []string{}, "values file to apply into Clusterfile")
 	fs.StringSliceVar(&arg.Sets, "set", []string{}, "set values on the command line")
-	fs.StringSliceVar(&arg.CustomEnv, "env", []string{}, "environment variables to set during command execution")
+	fs.StringSliceVar(&arg.CustomEnv, "env", []string{}, "environment variables to be set for images")
 	fs.StringSliceVar(&arg.CustomConfigFiles, "config-file", []string{}, "path of custom config files, to use to replace the resource")
 }
 
diff --git a/pkg/apply/gen.go b/pkg/apply/gen.go
index 3747280e7db..dd13558eab5 100644
--- a/pkg/apply/gen.go
+++ b/pkg/apply/gen.go
@@ -26,6 +26,7 @@ import (
 	"github.com/labring/sealos/pkg/runtime/factory"
 	"github.com/labring/sealos/pkg/types/v1beta1"
 	"github.com/labring/sealos/pkg/utils/iputils"
+	"github.com/labring/sealos/pkg/utils/logger"
 )
 
 func NewClusterFromGenArgs(cmd *cobra.Command, args *RunArgs, imageNames []string) ([]byte, error) {
@@ -43,6 +44,11 @@ func NewClusterFromGenArgs(cmd *cobra.Command, args *RunArgs, imageNames []strin
 	if err := c.runArgs(cmd, args, imageNames); err != nil {
 		return nil, err
 	}
+	if flagChanged(cmd, "env") {
+		logger.Info("setting global envs for cluster, will be used in all run commands later")
+		v, _ := cmd.Flags().GetStringSlice("env")
+		cluster.Spec.Env = append(cluster.Spec.Env, v...)
+	}
 
 	img, err := genImageInfo(imageNames[0])
 	if err != nil {
diff --git a/pkg/clusterfile/clusterfile.go b/pkg/clusterfile/clusterfile.go
index 95063f86912..100adeb837d 100644
--- a/pkg/clusterfile/clusterfile.go
+++ b/pkg/clusterfile/clusterfile.go
@@ -31,7 +31,6 @@ type ClusterFile struct {
 	customValues             []string
 	customSets               []string
 	customEnvs               []string
-	setDefaults              bool
 
 	cluster       *v2.Cluster
 	configs       []v2.Config
@@ -61,12 +60,6 @@ func (c *ClusterFile) GetRuntimeConfig() runtime.Config {
 
 type OptionFunc func(*ClusterFile)
 
-func WithSetDefaults(v bool) OptionFunc {
-	return func(c *ClusterFile) {
-		c.setDefaults = v
-	}
-}
-
 func WithCustomConfigFiles(files []string) OptionFunc {
 	return func(c *ClusterFile) {
 		c.customConfigFiles = files
diff --git a/pkg/clusterfile/pre_process.go b/pkg/clusterfile/pre_process.go
index e1c7a5351a0..cf561d8ca0c 100644
--- a/pkg/clusterfile/pre_process.go
+++ b/pkg/clusterfile/pre_process.go
@@ -17,8 +17,6 @@ package clusterfile
 import (
 	"bytes"
 	"errors"
-	"os"
-	"strings"
 
 	"helm.sh/helm/v3/pkg/cli/values"
 	"helm.sh/helm/v3/pkg/getter"
@@ -45,12 +43,6 @@ func (c *ClusterFile) Process() (err error) {
 	}
 	c.once.Do(func() {
 		err = func() error {
-			for i := range c.customEnvs {
-				kv := strings.SplitN(c.customEnvs[i], "=", 2)
-				if len(kv) == 2 {
-					_ = os.Setenv(kv[0], kv[1])
-				}
-			}
 			clusterFileData, err := c.loadClusterFile()
 			if err != nil {
 				return err
@@ -161,7 +153,7 @@ func (c *ClusterFile) DecodeRuntimeConfig(data []byte) error {
 	if cfg != nil {
 		c.runtimeConfig = cfg
 	} else {
-		kubeadmConfig, err := types.LoadKubeadmConfigs(string(data), c.setDefaults, decode.CRDFromString)
+		kubeadmConfig, err := types.LoadKubeadmConfigs(string(data), false, decode.CRDFromString)
 		if err != nil {
 			return err
 		}