Islanded DC microgrid systems need to be configured with multiple DESUs to cope with different load demands and energy fluctuations. Considering DESUs with different capacities, the SOC balancing effect is seriously affected due to the impedance mismatch in the line; for this reason, a multi-storage SOC balancing control strategy considering different capacities is proposed. Firstly, the relationship between SOC and the droop coefficient is established by an exponential function containing an acceleration factor, which improves the sensitivity of the droop coefficient to the late change of SOC balancing and realizes the adaptive adjustment of the droop coefficient. Each DESU only exchanges state information with neighboring nodes through a sparse communication network and adopts a dynamic consistency algorithm to obtain the global average state information. A multi-objective controller is designed, capable of compensating bus voltage dips while achieving accurate distribution of load power, eliminating the effect of mismatched line resistance, reducing the control process, and alleviating the system communication burden. Finally, a simulation model is built based on MATLAB/Simulink software, and the effectiveness of the proposed control strategy is confirmed under various complex operating conditions.