Owning to the power battery pack in the all-electric ship is vulnerable to transient large current and short service life, a scheme of composite energy storage system with lithium iron phosphate battery and super-capacitor as the core was proposed. According to the theoretical analysis result, DC/DC converter was adopted to make good use of the super-capacitor. The second-generation non-dominated sorting genetic algorithm with elite strategy was used for multi-objective optimization to realize the optimal configuration of energy storage system with the help of energy management strategy. The simulation results showed that the proposed scheme combined with the energy management strategy based on fuzzy control can meet the requirement of the variable load well.