Nearest level modulation is a common modulation method for Modular Multilevel Converters (MMC). As the number of modules is few or the modulation voltage is low, the output current is distorted. Firstly, this paper theoretically analyzes the reason why the harmonic of output current is distorted in MMC, and then proposes a control method to suppress the harmonics. The method extracts the harmonics of output current, and through a proportional integral regulator, the negative harmonic voltages is obtained. Lastly, the harmonic voltages are added to the modulation reference voltage. The purpose of this method is to obtain the total reference voltage. The proposed method is simple, feasible, and easy to implement. The simulation and experimental results show that the distortion of the output current of MMC is suppressed by the proposed method.