As the increase of power and voltage level of back-to-back three-level neutral-point clamped (NPC) converters, the high-amplitude and high-frequency common-mode voltage (CMV) has become an urgent problem. To address this, a CMV elimination method based on pulsewidth modulation pulse alignment for back-to-back three-level NPC converter is proposed. On this basis, a neutral-point potential balance method based on zero-sequence voltage (ZSV) is also proposed. In order to decouple the CMV elimination and the neutral-point potential balance, the same optimal ZSV is injected into both the rectifier and inverter sides, and the CMV elimination will not be affected. Simulation and experiments are presented to verify the effectiveness of the proposed method.