A stand-alone multi-microgrid (MMG) system can be formed by connecting multiple stand-alone microgrids (MGs). In the stand-alone MMG system where the frequencies of each MG system are different, a back-to-back (BTB) converter can be used for interconnecting the adjacent MG system. The frequency control performance of the MMG system can be improved by designing the suitable controller of the BTB converter. This study proposes a multi-frequency control in the BTB converter to improve the performance of frequency regulation in the MMG system. Autonomous power sharing between each MG system is achieved by using the proposed multi-frequency control. The stand-alone MMG system where two stand-alone MG systems with different nominal frequencies are interconnected using the BTB converter is simulated in this study to show the feasibility of the proposed multi-frequency controller. Each stand-alone MG system consists of an inverter-based distributed generator (DG) that uses a grid-forming converter with a conventional frequency droop controller. The inverter-based DG is responsible for the primary frequency control in each MG system. To show the effectiveness of the proposed multi-frequency control, a comparison study of the multi-frequency control and the single frequency control is presented in this study. Simulation results show that the system stability can be improved by using the proposed multi-frequency controller.