In order to solve the problem of the unbalance of State of Charge (SOC) in a distributed energy storage system in DC microgrid, a balancing control strategy for distributed energy storage of an island DC microgrid is proposed. The scheme adopts a logarithmic form to design a reference voltage function, and takes the ratio of the SOC of a single energy storage unit and the SOC average of all energy storage units as a logarithmic function input. This means that the reference voltages vary approximately symmetrically with respect to the rated bus voltage in the charging and discharging process of each energy storage unit without the bus voltage offset. On this basis, the proportional relationship between the output power of the energy storage unit and its reference voltage is simplified to the parameter selection process. The stability of the system is judged by Lyapunov’s first method. Finally, the correctness and practicability of the proposed control strategy are verified by Matlab/Simulink and experiment. This work is supported by National Natural Science Foundation of China (No. 51577162).