In order to optimize the capacity allocation of the energy storage system and improve the power supply reliability and economy of the DC micro-grid cluster, a joint optimal allocation method of independent DC micro-grid cluster hybrid energy storage is proposed in this paper, in which each sub-grid is considered as a standby. Firstly, the optimal objective is to minimize the annual cost of the overall investment, operation and maintenance of the DC micro-grid cluster hybrid energy storage, and a hybrid energy storage capacity allocation model is established. Secondly, the configuration cost of hybrid energy storage is further reduced without losing the independence of the configuration of the hybrid energy storage capacity of each sub-micro grid. Finally, taking a double DC micro-grid cluster as an example, the results illustrate the advantage of micro-grid cluster of interconnected power by comparing the independent optimization and configuration of joint optimization.By applying the joint optimal allocation method, it greatly reduces investment cost of hybrid energy storage system and improves the micro-grid cluster of running stability. The superiority of the proposed configuration method is proved with the independent model of DC micro-grid cluster of planning and construction to provide certain scientific basis.