In order to ensure the normal work of Modular Multilevel Converters (MMC) and realize the capacitor voltage balancing, a sub-module controller in MMC control system is designed. First, the overall structure and working principle of MMC control system are described and effect of the sub-module controller in MMC control system is introduced. Then the design of main hardware modules and software module of the sub-module controller is presented, the implementation of the undervoltage and overcurrent protection for IGBT in hardware and PWM driven pulse with dead zone protection generated by using software are emphatically introduced. Finally, the rationality and feasibility of the sub-module controller is verified based on DC-AC converter of MMC experimental platform.