When the motor train auxiliary converter runs in the line with high harmonic content, the fault occurs frequently. The test results show that there is a correlation between the high harmonic content of the traction network and the failure of the start. In order to study the influences of the high order harmonics of traction network for the precharging process of the EMU auxiliary converter, the harmonic model of locomotive transformer is established to analyze the permeability characteristics of high-order harmonics for the EMU auxiliary converter system, and the harmonic model of auxiliary converter filter circuit is established to analyze the series resonance. The mathematical model of single-phase capacitor-filtered diode bridge rectifier circuit is presented to analyze the influences of the high order harmonics for DC side voltage. The CRH EMU auxiliary converter with starting fault is measured, and the harmonic measured data are analyzed. Then the computer simulation model of the EMU auxiliary converter is built by Matlab/Simulink to analyze the influences of the high order harmonics of traction network for the precharging process of the EMU auxiliary converter. The results illustrate that the high-order harmonic voltage in the traction network could easily penetrate into the EMU auxiliary converter system, the high-order harmonic voltage nearby filter circuit series resonance frequency will excite series resonance to lead to serious distortion of filter capacitor voltage, which can lead to the DC side voltage increase and auxiliary converter precharging start fault. It is of certain reference meaning for deeply researching the characteristic of EMU auxiliary converter and selection of filter circuit component under harmonic environment. This work is supported by Fundamental Research Funds for the Central Universities (No. A0920502051619-34).