Abstract: In view of the slow response speed of fuel cells, which limits their ability to promptly respond to dynamic power loads, a composite energy storage power supply is employed to address this issue. Using wavelet transform technology, the steady component of the load is allocated to the fuel cell, while the fluctuating portion is assigned to the composite power supply. Based on Pontryagin’s minimum principle, an energy management strategy is formulated with the supercapacitor’s energy as the state variable, the output power of the lithium battery as the control variable, and the root mean square current of the lithium battery as the cost function. A simulation model of the ship power system is built in Matlab/Simulink to validate the proposed energy management strategy. The results demonstrate that the proposed control strategy enables stable output power from the fuel cell and achieves rational power distribution according to the charge-discharge characteristics, capacity, and current state of charge of both the supercapacitor and the lithium battery. Compared to hybrid ships without supercapacitors and traditional fixed filter strategies, the proposed approach reduces the rate of current change in the lithium battery and extends the service life of the fuel cell and lithium battery.