Aiming at the random and intermittent characteristics of the distributed power supply in the microgrid, a method to optimize the configuration of the composite energy storage capacity is proposed to ensure its economical and reliable operation. This paper proposes a method for optimizing the configuration of composite energy storage capacity. Firstly, an optimization configuration model of composite energy storage capacity is established to establish a multi-objective function with the lowest life cycle cost of the composite energy storage system, the best smooth power of renewable energy, the highest utilization of the micro-net connection line, and the highest reliability of power supply. The constraints of the composite energy storage system, the tie-line transmission power constraints, the micro-turbine output power constraints, and the renewable energy power constraints are constraints. Secondly, a modified whale optimization algorithm was used to obtain the optimal configuration of the composite energy storage, and compared with the basic whale algorithm and the particle swarm algorithm. Finally, the results of this paper are compared with the basic whale algorithm and particle swarm algorithm by an example. Verification of differential evolution whale algorithm can more rationally configure composite energy storage capacity. It allows the wind power fluctuations to be more effectively suppressed. At the same time, the utilization ratio of the micro-network connection line has also been improved, and the rational use of resources has been realized.