For three-level VIENNA rectifier, several low-order harmonics will emerge in the input current due to the distortion near the zero-crossing point and the fluctuation in the output voltage. In this paper, a new control strategy, including a dual-loop and a balance loop, is established based on the state-space average model in stationary αβ frame to achieve reduced input current harmonics. As to the inner current loop, the proportional-resonant (PR) control is selected for it does not require complicated frame transformation and can track the AC signals with zero error. Moreover, the design of the PR controllers is discussed in detail according to the Bode diagram. During the process of discretization, the Tustin with pre-warping is preferred considering the resonant peak displacement. Finally, the correctness and effectiveness of the proposed control scheme are verified by simulation and experiment results.