Abstract: Hybrid Energy Storage System（HESS） can improve the lifetime loss of fuel cells caused by ship load power fluctuation, but the configuration cost limits the wide application of HESS in fuel cell ships. In order to rationally allocate energy storage capacity and make ship power system design have long-term reliability, this paper proposes a capacity optimal allocation method which takes into account the whole life cycle of HESS. Based on the model of each power supply system, the life-cycle cost model of HESS including purchase cost, maintenance cost, replacement cost and energy consumption cost is established, and the rain-flow counting method is used to evaluate the replacement cost of energy storage. Finally, according to the typical power demand data of "Alsterwasser" fuel cell ship, the capacity parameters of energy storage equipment, the output power of fuel cells and the operation parameters of power system are taken as optimization variables, and the gray Wolf optimization algorithm is used to solve the problem. Through the comparison of configuration schemes under different energy storage types and optimization objectives, the economic efficiency of the proposed method is verified.