the issue is resolved.the issue is caused by transaction time out of windows service manager.
And there is another registry value to control the transaction time out value. ServicesPipeTimeout
The default time out value is 30 seconds. after change the value the service can stop gracefully. follow http://cid-6398bdbc2043a117.spaces.live.com/blog/cns!6398BDBC2043A117!113.entry to change the value.