Aiming at the mutual restriction of life loss and economic cost of ship energy storage system, this paper proposes a method of ship energy storage system configuration optimization based on multi-objective genetic algorithm. A multi-objective optimization model with life loss and economic cost as the objective function is established. A multi-objective genetic algorithm is used to find a set of Pareto optimal solution sets, and the optimal compromise solution is selected from the Pareto optimal solution set through the TOPSIS algorithm. Finally, using the MATLAB platform's powerful simulation function and simple language features, the dual-fuel generator set electric propulsion ship micro-grid system is used as the research object, and a simulation example is designed. The results show that in the application of the ship energy storage system, after the optimization of the algorithm, the economic cost increased by 0.97%, but the life loss was reduced by 8.7%, which can effectively reduce the life loss while controlling the economic cost almost unchanged , Taking into account the service life and economic benefits of the ship's energy storage system. It is verified that the optimal configuration method in this paper is effective and has important reference value for the optimization of energy storage system configuration in actual production applications.