The Modular Multilevel Converter Based Battery Energy Storage System (MMC-BESS) can output active and reactive power at the same time. This is suitable for new energy grid connection with medium-high voltage and high power occasions. In order to solve the problem of unbalanced State of Charge (SOC) caused by the difference of energy storage units, a three-level balance control strategy of battery SOC is proposed. First, in view of the SOC difference between the phases, SOC balance is realized by changing the power of each phase by controlling the DC component of the bridge arm circulating current. Then, for the SOC difference of upper and lower bridge arms in the same phase, the SOC balance is realized by changing the power of the upper and lower bridge arms through controlling the fundamental frequency component of the circulating current. Finally, for the SOC difference of the sub-modules in the same bridge arm, the SOC balance is achieved by changing the power of the sub-modules by reconstructing the modulation wave. Experimental results verify the effectiveness of the control strategy. This work is supported by the National Natural Science Foundation of China (No. 51807073).