The permanent magnet traction system suitable for serialized Chinese standard metro trains is the development direction of the new generation of rail transit traction systems. The rotor initial position of the permanent magnet synchronous motor (PMSM) determines the size of the starting torque, and the polarity of the magnetic pole determines the direction of the starting torque. So the accuracy of rotor initial position identification is related to whether the motor can start stably and accelerate smoothly. Based on the analysis of the mathematical model of PMSM, the initial estimated position of the rotor is obtained by using the high frequency square wave voltage injection algorithm. Then a narrow positive and reverse voltage pulse is injected into the estimated d-axis, and the magnitude of the positive and reverse response current on the d-axis is compared to determine whether the positioned magnetic pole is the N pole or the S pole. If the magnetic pole is the S pole, the initial estimated position needs to be compensated to be positioned at the N pole. Simulink simulation and test results show that when the actual initial position of the motor is different, the algorithm can identify the correct rotor position. The maximum identification error is 0.052 4 rad, and the average error is 0.016 1 rad.