Modular Multilevel Converter (MMC) sub-module capacitor voltage balancing is a hot topic in current MMC research. Large number of single bridge arm submodules in MMC usually lead to the defects such as long controller operation time, frequent switching of sub-modules, and large switching loss leading to MMC failure. To solve above problems, this paper proposes a hybrid control strategy based on improved bubble sorting algorithm and voltage average comparison. According to monitor the capacitor voltage in real time, this paper adopts the improved bubble sorting algorithm to rank the capacitor voltage of the sub-modules during system initialization which can reduce operations and simulation time of MMC controller. The sub-module voltage average comparison strategy is adopted in the subsequent control cycle to switch the sub-module which can reduce the switching frequency. Finally, the 21-level MMC model is built on Matlab/Simulink. The simulation results prove the feasibility and effectiveness of the proposed hybrid control strategy. This work is supported by National Natural Science Foundation of China (No. 61603242) and Discipline Construction Project of Mechanical Electronic Engineering (No. 2018xk-A-03).