flow service and java service which one is better
I prefer to think of it like this- Why would you have spent the large sum of money that is the webMethods product suite, simply to turn around and write your services in Java? 
I see this question a lot from developers that are new to webMethods IS that come from a Java background (also get this from .Net developers). A lot developers will try and make webMethods IS behave or conform to what they know of Java or .Net which is a completely natural thing to do. Don’t do that however, it is a completely different animal.
There are times when you will need to write some Java utility services in webMethods IS but that should be the exception not the rule.
I agree with Mark’s comments.
As Mark implies, FLOW is the “native” language for Integration Server. Most of your work should be done using FLOW, with Java used from time to time for specific and focused needs.
Search the forums for additional discussions on Java and FLOW services–there have been many in depth discussions on this topic in the past.