A fiber-based，high precision long-term stable time synchronization system for multi-channel laser pulses is presented，using fiber pulse stacker combined with high-speed optical-electrical conversion and electronics processing technology. This scheme is used to synchronize two individual lasers including a mode-lock laser and a time shaping pulse laser system. The relative timing jitter between two laser pulses achieved with this system is 970 fs (rms) in five minutes and 3.5 ps (rms) in five hours. The synchronization system is low cost and can work at over several tens of MHz repetition rate.