For electric locomotive passing neutral section system, the magnetizing inrush current has adverse effect both on the electric locomotive itself and the power quality of traction power system. A new principle of electric locomotive inrush current elimination system based on high power electronic technology is proposed, meanwhile two kinds of PWM modulation voltage algorithms, namely cophase amplitude modulation and frequency conversion phase shift, are presented. By controlling the new high power electronic circuit rectifier, inverter, frequency conversion mode and locomotive transformer excitation voltage at different times, it achieves electric locomotive non-inrush passing neutral section and removes the inrush current when the transformers are switched on. Using the proposed method, the simulation model of electric locomotive transformer for passing neutral section is established. Simulation results show that two kinds of voltage modulation algorithms can effectively inhibit the switching inrush current generation, verifying the effectiveness of this method. This work is supported by National Natural Science Foundation of China (No. 51607106).