In order to improve the energy efficiency and reduce emissions of ship, both of the diesel generator and fuel cell are used to supply power to the hybrid ship, in which the engine provides the basic load, and the rest power is provided by the fuel cell when the ship power load demand is greater than the basic load. Ship power transmission model and optimized performance indicators which can be calculated are deduced. The model of the ship electric propulsion system with energy storage units is established based on Matlab/Simulink. The simulation results show that the running efficiency of diesel engine is improved, satisfying the power demand of ship by use of new energy controller and improving the stability of the system.