In a dual-sampling-rate control system, the difference between the sampling frequency of the motor control algorithm and that of the pulse modulation control leads to a phase error between the controlled reference voltage vector phase and the actual voltage vector phase of the motor. Aiming at the voltage phase mismatch problem caused by the dual-sampling-rate control system in rail transit, a voltage phase regulator suitable for permanent magnet synchronous motor (PMSM) traction drive systems is proposed to suppress the voltage phase error. Based on the multi-sampling-rate control theory, this paper models the voltage phase response under the variable-ratio dual-sampling-rate control system. Through analysis of the error mechanism, a proportional voltage phase regulator is proposed, and parameter optimization design is implemented to achieve suppression of the voltage phase error. Stability analysis using discrete control theory optimizes the delay compensation. Verification results based on the PMSM traction drive system demonstrate that the proposed method not only reduces control delay but also enhances the steady-state torque output capability and dynamic response capability.