diff --git a/pkg/custompluginmonitor/plugin/plugin.go b/pkg/custompluginmonitor/plugin/plugin.go
index 0b90e9c01..9f9cad32b 100644
--- a/pkg/custompluginmonitor/plugin/plugin.go
+++ b/pkg/custompluginmonitor/plugin/plugin.go
@@ -17,7 +17,6 @@ limitations under the License.
 package plugin
 
 import (
-	"context"
 	"fmt"
 	"io"
 	"os/exec"
@@ -143,15 +142,15 @@ func readFromReader(reader io.ReadCloser, maxBytes int64) ([]byte, error) {
 }
 
 func (p *Plugin) run(rule cpmtypes.CustomRule) (exitStatus cpmtypes.Status, output string) {
-	var ctx context.Context
-	var cancel context.CancelFunc
+	isTimeout := false
+	isHung := false
 
+	var timeoutDuration time.Duration
 	if rule.Timeout != nil && *rule.Timeout < *p.config.PluginGlobalConfig.Timeout {
-		ctx, cancel = context.WithTimeout(context.Background(), *rule.Timeout)
+		timeoutDuration = *rule.Timeout
 	} else {
-		ctx, cancel = context.WithTimeout(context.Background(), *p.config.PluginGlobalConfig.Timeout)
+		timeoutDuration = *p.config.PluginGlobalConfig.Timeout
 	}
-	defer cancel()
 
 	cmd := util.Exec(rule.Path, rule.Args...)
 
@@ -170,37 +169,6 @@ func (p *Plugin) run(rule cpmtypes.CustomRule) (exitStatus cpmtypes.Status, outp
 		return cpmtypes.Unknown, "Error in starting plugin. Please check the error log"
 	}
 
-	waitChan := make(chan struct{})
-	defer close(waitChan)
-
-	var m sync.Mutex
-	timeout := false
-
-	go func() {
-		select {
-		case <-ctx.Done():
-			if ctx.Err() == context.Canceled {
-				return
-			}
-			klog.Errorf("Error in running plugin timeout %q", rule.Path)
-			if cmd.Process == nil || cmd.Process.Pid == 0 {
-				klog.Errorf("Error in cmd.Process check %q", rule.Path)
-				break
-			}
-
-			m.Lock()
-			timeout = true
-			m.Unlock()
-
-			err := util.Kill(cmd)
-			if err != nil {
-				klog.Errorf("Error in kill process %d, %v", cmd.Process.Pid, err)
-			}
-		case <-waitChan:
-			return
-		}
-	}()
-
 	var (
 		wg        sync.WaitGroup
 		stdout    []byte
@@ -220,14 +188,46 @@ func (p *Plugin) run(rule cpmtypes.CustomRule) (exitStatus cpmtypes.Status, outp
 	}()
 	// This will wait for the reads to complete. If the execution times out, the pipes
 	// will be closed and the wait group unblocks.
-	wg.Wait()
+	// If the timeout is caused by the plugin process or sub-process hung due to GPU device errors or other reasons,
+	// wg.Wait() will be blocked forever, so we need to add a timeout to the wait group.
+	waitChan := make(chan struct{})
+	go func() {
+		wg.Wait()
+		close(waitChan)
+	}()
+	select {
+	case <-waitChan:
+		// The reads are done.
+		break
+	case <-time.After(timeoutDuration):
+		klog.Errorf("Waiting for command output timed out when running plugin %q", rule.Path)
+		isTimeout = true
+		err := util.Kill(cmd)
+		if err != nil {
+			klog.Errorf("Error when killing process %d: %v", cmd.Process.Pid, err)
+		} else {
+			klog.Infof("Killed process %d successfully", cmd.Process.Pid)
+		}
 
-	if stdoutErr != nil {
+		// Check if the process is in D state. If it is, the process is hung and can not be killed.
+		// It also means that the plugin can not report the correct status, instead reports Unknown status.
+		// On a GPU machine, a plugin with Python script calling pynvml API may hang in D state due to some GPU device errors.
+		if util.IsProcessInDState(cmd.Process.Pid) {
+			klog.Errorf("Process %d is hung in D state", cmd.Process.Pid)
+			isHung = true
+		}
+	}
+
+	if isHung {
+		return cpmtypes.Unknown, fmt.Sprintf("Process is hung when running plugin %s", rule.Path)
+	}
+
+	if !isTimeout && stdoutErr != nil {
 		klog.Errorf("Error reading stdout for plugin %q: error - %v", rule.Path, err)
 		return cpmtypes.Unknown, "Error reading stdout for plugin. Please check the error log"
 	}
 
-	if stderrErr != nil {
+	if !isTimeout && stderrErr != nil {
 		klog.Errorf("Error reading stderr for plugin %q: error - %v", rule.Path, err)
 		return cpmtypes.Unknown, "Error reading stderr for plugin. Please check the error log"
 	}
@@ -239,16 +239,13 @@ func (p *Plugin) run(rule cpmtypes.CustomRule) (exitStatus cpmtypes.Status, outp
 		}
 	}
 
-	// trim suffix useless bytes
-	output = string(stdout)
-	output = strings.TrimSpace(output)
-
-	m.Lock()
-	cmdKilled := timeout
-	m.Unlock()
-
-	if cmdKilled {
-		output = fmt.Sprintf("Timeout when running plugin %q: state - %s. output - %q", rule.Path, cmd.ProcessState.String(), output)
+	stderrStr := ""
+	if isTimeout {
+		output = fmt.Sprintf("Timeout when running plugin %q: state - %s. output - %q", rule.Path, cmd.ProcessState.String(), "")
+	} else {
+		// trim suffix useless bytes
+		output = strings.TrimSpace(string(stdout))
+		stderrStr = strings.TrimSpace(string(stderr))
 	}
 
 	// cut at position max_output_length if stdout is longer than max_output_length bytes
@@ -259,13 +256,13 @@ func (p *Plugin) run(rule cpmtypes.CustomRule) (exitStatus cpmtypes.Status, outp
 	exitCode := cmd.ProcessState.Sys().(syscall.WaitStatus).ExitStatus()
 	switch exitCode {
 	case 0:
-		logPluginStderr(rule, string(stderr), 3)
+		logPluginStderr(rule, stderrStr, 3)
 		return cpmtypes.OK, output
 	case 1:
-		logPluginStderr(rule, string(stderr), 0)
+		logPluginStderr(rule, stderrStr, 0)
 		return cpmtypes.NonOK, output
 	default:
-		logPluginStderr(rule, string(stderr), 0)
+		logPluginStderr(rule, stderrStr, 0)
 		return cpmtypes.Unknown, output
 	}
 }
diff --git a/pkg/util/exec_unix.go b/pkg/util/exec_unix.go
index d7311ba3f..a8f52e625 100644
--- a/pkg/util/exec_unix.go
+++ b/pkg/util/exec_unix.go
@@ -21,6 +21,8 @@ package util
 import (
 	"fmt"
 	"os/exec"
+	"strconv"
+	"strings"
 	"syscall"
 )
 
@@ -42,3 +44,13 @@ func Kill(cmd *exec.Cmd) error {
 	}
 	return syscall.Kill(-cmd.Process.Pid, syscall.SIGKILL)
 }
+
+// IsProcessInDState checks if the process is in D state.
+func IsProcessInDState(pid int) bool {
+	// "-o stat=" is used to get the process state without the header.
+	cmd := exec.Command("ps", "-o", "stat=", "-p", strconv.Itoa(pid))
+	if res, err := cmd.Output(); err == nil && strings.Contains(string(res), "D") {
+		return true
+	}
+	return false
+}
diff --git a/pkg/util/exec_windows.go b/pkg/util/exec_windows.go
index 3e70d6f23..e11cca264 100644
--- a/pkg/util/exec_windows.go
+++ b/pkg/util/exec_windows.go
@@ -86,3 +86,8 @@ func Kill(cmd *exec.Cmd) error {
 	}
 	return err
 }
+
+// IsProcessInDState does not apply to Windows.
+func IsProcessInDState(pid int) bool {
+	return false
+}