Modular multilevel converter with integrated battery energy storage system (MMC-BESS) has been proposed for energy storage requirements in high-voltage applications. The state-of-charge (SOC) equilibrium of batteries is essential for BESS to guarantee the capacity utilization. However, submodule voltage regulation can lead to over-modulation of individual submodules, which will limit the efficiency of SOC balancing control. Focusing on this problem, a modified SOC balancing control method with high efficiency is proposed in this paper. The tolerance for battery power unbalance is defined to quantize the convergence of SOC balancing control. Both the DC component and AC component are considered while regulating submodule voltage. The linear programming method is introduced to realize the maximum tolerance for battery power unbalance in different operation modes. Based on the analysis, by choosing appropriate submodule voltage regulation method, the efficiency of SOC balancing control is improved greatly. In addition, the SOC controller is also optimally designed to avoid over-modulation of submodules. Finally, the detailed simulation and experiment results verify the effectiveness of the analysis and proposed control strategy.