Excessive computation is required in the controller of modular multilevel converter (MMC) when existing large amount of sub-modules per arm. This will also result in a decline in the running speed of the system and even affect dynamic performance. To solve this problem, a capacitor voltage balancing strategy based on the quicksort algorithm is proposed. Through divide and conquer technology, modular voltage sequences based on comparison and division. The modules put into operation are decided by capacitor energy variation to realizes voltage balanced. Time complexity and sort efficiency are deduced and the effect on system performance is analyzed. The adaptability of the strategy under different circumstances is researched. The DSP controller TMS320F28335 is used to measure execution time of algorithms. The MMC model is set up on the PSCAD/EMTDC and the efficiency and correctness of the voltage balancing strategy based on quicksort are proved. The simulation results show that the quicksort algorithm can reduce computation time, lower the requirement of the hardware and advantages become more obvious with the increasement of sub-module.