This paper focuses on designing a power allocation strategy for a fuel cell ship. The performance of the fuel cell varies during operation, so a power allocation strategy considering fuel cell performance differences is proposed, which consists of two layers. In the first layer, the maximum power and maximum efficiency of each fuel cell system (FCS) are updated in real-time with an online parameter identification model, which is composed of the fuel cell semi-empirical model and adaptive Kalman filter. The second layer takes the state of charge of the battery energy storage system, the maximum power, and the maximum efficiency as inputs for power allocation. Compared with the equal allocation strategy and daisy chain strategy, the total hydrogen consumption reduces by 5.3% and 15.1% and the total output power of the FCS with poor performance reduces by 14.1% and 15.7%. The results show that the proposed method can improve the efficiency of the ship power system and reduce the operational burden of the FCS with poor performance.