With outstanding advantages compared to LCC and conventional VSC structures, the MMC topology has been increasingly applied in HVDC transmission systems in recent years, including MMC-based back-to-back HVDC system. However, because this system is used to interconnect two asynchronous AC power systems (usually with different frequencies), the amount of non-characteristic harmonics is generated in this system. And if these non-characteristic harmonics are not removed, they can propagate to linked AC power systems and can cause many harmful effects on these systems. This paper proposes a supplementary frequency control method to mitigate the non-characteristic harmonics generated in an MMC-based back-to-back HVDC system. Simulation results verify the effectiveness of the proposed method. The proposed method can be applied to prevent potential resonances in the system as well as improving the reliability and safety of the entire connected system.