Abstract. This paper presents a three phase cascaded multilevel inverter based supercapacitor (SC) energy storage system with novel structure and control strategy to maintain the energy balance of between phases. Every two phases are coupled with a series LC filter. With the filter, SC cells in different phases could exchange energy with an auxiliary power flow at high frequency. The auxiliary power flow is orthogonal to the primary power flow. The phase difference between high frequency voltage and current components of each phase determines whether the energy is absorbed into or released from its SC cells. Unlike traditional energy balancing strategies, the proposed method is independent to the fundamental real power drawn by the energy storage system. Simulation results confirmed the effects of proposed theories.