Aiming at the problem that the negative sequence component of AC current is generated when the AC side voltage is unbalanced in grid-connected AC-DC hybrid microgrid, which leads to the double frequency fluctuation of DC bus voltage, a fractional order sliding mode control method of DC bus voltage and negative sequence current suppression method of AC side are proposed. First, based on the mathematical model of AC-DC hybrid microgrid interconnecting interface converter when the grid voltage is unbalanced in synchronous rotating coordinate system, the outer voltage loop variable structure sliding mode controller is designed. Then, according to the power transmission characteristics of the interconnected interface converter when the voltage is unbalanced, the positive sequence component of the three-phase voltage on the AC side is extracted, and the negative sequence current suppression command on the AC side is obtained. Next, the fractional order sliding mode reaching law is used to design the inner loop current decoupling controller, and the Lyapunov function is used to verify the stability. Finally, the AC/DC hybrid microgrid model built on Matlab/Simulink verifies that compared with the traditional PI control, the proposed control strategy not only restrains the three-phase current imbalance, but also improves the response speed by nearly 50%.