In view of the problems of power fluctuation of fuel cell and extreme State of Charge (SOC) polarization of energy storage unit in composite energy supply system of fuel cell ship, according to the topological structure of the system, the design of control strategy for composite energy supply system is proposed based on the combination of load power frequency distribution and fuzzy logic control method. The advantages of the design are verified with an example simulation. The results show that the design can keep the output power of fuel cell smooth effectively and is of a good balance control effect on SOC of energy storage unit.