To simultaneously solve the problems of the state-of-charge (SOC) equalization and accurate current distribution among distributed energy storage units (DESUs) with different capacities in isolated DC microgrids, a multi-storage DC microgrid energy equalization strategy based on the hierarchical cooperative control is proposed. In the primary control layer, the link between the droop coefficient and SOC is established through a logarithmic function, and the droop coefficient is adaptively adjusted according to the SOC value in order to achieve fast SOC equalization. In the secondary control layer, by designing a coordinated state factor, only one PI controller is required to eliminate the influence of the line impedance on the accurate distribution of the output current and the DC bus voltage drop. In the communication layer, local nodes only need to communicate with neighboring nodes without the need for a central controller, and the dynamic consistency algorithm is used to obtain the average value information about the energy storage system (ESS). Finally, the feasibility and effectiveness of the proposed control strategy are verified by experimental analysis on the DC microgrid hardware-in-the-loop experimental platform.