In order to optimize the energy management strategy and solve the problem of the power quality degradation of fuel cell hybrid electric ships, a particle swarm optimization algorithm based energy management strategy is proposed in this paper. Taking a fuel cell ship as the target ship, a system simulation model is built in Matlab/Simulink to verify the proposed energy management strategy. Through simulations and comparisons, the bus voltage curve of the optimized hybrid power system fluctuates more gently, and the voltage sag is smaller. The amplitude of the voltage fluctuation under maneuvering conditions is reduced by 55% compared with that of the original ship. The charging and discharging process of the composite energy storage system is optimized under maneuvering conditions, the power quality of the marine power grid is improved, and the use of the energy management strategy can extend the service life of the battery.