Based on conventional H-bridge topologies of magnet power supplies, a high-frequency common-mode equivalent model was established. It is pointed out that the two phase legs have complementary effect of common-mode noise under bipolar PWM switching. Due to the phase difference of the driving pulses in the real product, however, the common-mode cancellation effect is greatly affected. Based on the common-mode equivalent model, a frequency domain analysis was carried out to determine the theoretical relationship between the common-mode noise intensity and the phase difference, which can guide the adjustment of the driving pulses. It was also found that the increase of switching frequency will aggravate the common-mode noise caused by the phase difference. To reduce the common-mode noise, a method that automatic calibration of the driving pulses was evaluated by a simulation and experimentally. Finally, A magnet power supply experiment platform is built, and the experimental results show that this method can effectively reduce the common mode voltage.