when it comes to time history analysis，how to define the length of time for waterhammer working？For a single pipe，it maybe easy to go，what about a complex pipe system ？

No one said it would be easy.
Typically, the time history input for a hammer load works off the change in pressure between the upstream "elbow" and downstream "elbow" for each significant run of pipe (for each significant elbow-elbow pair). Extend your load and analysis time to include the returning pressure wave as it dies down.