Maintaining the branch energy balance poses a huge challenge to controller design of many modular multilevel converter (MMC) topologies. Aiming at railway traction power supply system application of a three-phase to single-phase MMC with equal input and output frequency, this article proposes a branch energy balance control with an improved common-mode voltage selection. As a result, the capacitor voltage oscillations as well as circulating currents are reduced greatly. As the MMC is a complicated periodic time-varying system, an average theory is used to simplify the analysis and controller design. The controllability analysis of the system is carried out and the results show that the proposed branch energy balance control is controllable under most load conditions. In addition, the stability of the branch energy balance system is validated through frequency response. Finally, experimental results verify the effectiveness of the control scheme by an 18-cell model based on the RT-LAB platform.