Because of the volatility of accessing distributed new energy, it is necessary to configure energy storage equipment with a certain capacity for an isolated DC microgrid. To prevent excessive discharge or deep charging of distributed energy storage units, it is necessary to ensure that the state of charge (SOC) of the energy storage units is balanced during charging and discharging. To achieve this, a distributed control strategy of an energy storage unit considering communication anomaly is proposed. For energy storage units with different rated capacities, the traditional droop control is improved, and the droop coefficient is periodically modified using a sample holder until the SOC of the energy storage unit is balanced. Using the voltage and current information to generate a single compensation loop, the output current is distributed in proportion to the rated capacity and the DC bus voltage is compensated, reducing the requirements of the system communication capability. In the case of communication failure, the Dijkstra algorithm is used to update the topology matrix, and the information of adjacent nodes is obtained based on the improved dynamic consistency algorithm to obtain the average value of information under the new communication topology. The stability of the system is verified by frequency domain analysis. Finally, four case study models are built in the RTLAB platform to verify the effectiveness of the proposed control strategy.