Due to the application of the single-phase power supply mode in the traction drive system of high-speed EMU, the DC output voltage of the single-phase pulse rectifier is superimposed with an AC ripple voltage component which the frequency is twice the grid frequency. The AC ripple voltage component may cause the traction motor to generate the current beat phenomenon, resulting in problems such as three-phase unbalance of the traction motor current and increased torque ripple. Aiming at the phenomenon, a beat-less control algorithm based on frequency domain analysis was proposed. The algorithm was based on the formation mechanism of beat frequency and theoretical analysis of output voltage harmonics, and frequency compensation was achieved by superimposing a function mapping the DC voltage ripple component on the output frequency of traction inverter, which eliminated the low frequency harmonic components effectively. Combined with vector control system, the simulation and experimental verification of the algorithm were completed. The simulation and experimental results showed that the proposed method could effectively suppress the motor beat phenomenon.