This article proposes a novel state of charge (SoC) balancing control strategy based on multi-agent control between distributed the battery energy storage systems (BESSs) in super-UPS. The proposed control strategy has plug and play capability. Batteries with different capacities are considered in the control system. The battery capacity degradation under long term operation is further taken into account. In addition, a model-free iPI control strategy is designed for primary current control to achieve the tracking response of BESS to the reference current. Firstly, the distributed voltage and per-unit current dynamic consensus algorithm is introduced to maintain the DC bus voltage and achieve the battery current sharing. Then, a SoC balancing algorithm based on multi-agent control strategy is proposed. Furthermore, an adaptive capacity estimation algorithm is proposed considering the battery capacity degradation. The efficiency of the proposed control strategy is demonstrated in MATLAB/Simulink.