Multi-level converters are widely applied in DC microgrids because of their capability to reduce the voltage stress on switches and the volumes of filtering inductors and filtering capacitors. Since the flying-capacitance voltage and output voltage of a three-level Buck converter are coupled, the converter is a nonlinear system with strong coupling of multi-input and multi-output. To solve this problem, a decoupled backstepping sliding mode control method for inverse system is proposed in this paper. The inverse system method is used to decouple the output voltage control and flying-capacitance voltage control, and the backstepping sliding mode control method is used to ensure the stability and robustness of output voltage. The flying-capacitance voltage is balanced at 1/2 of the input voltage by the state feed-back control. Simulation and experimental results show that the proposed control strategy can achieve satisfying steady-state and dynamic characteristics of flying-capacitance voltage and output voltage.