The permanent magnet synchronous motor (PMSM) offers high efficiency, high power density, and strong overload capacity as its main advantages. However, its operating characteristics under railway operating conditions are still unclear. Given that the harmonics of traction current during the operation of the permanent magnet motor electric locomotive may cause interference to the track circuit, its harmonic distribution generated in the operating frequency band of the track circuit needs to be studied urgently. In this paper, a new type of permanent magnet direct-drive electric locomotive is taken as the research object, and three typical working conditions of acceleration, uniform speed and braking are carried out in the field test, and then, the data are analyzed for the characteristics of traction harmonic current. Based on the MATLAB platform, the time domain of the measured data is carried out to determine the waveform characteristics. In order to reduce the signal spectral leakage, the Hanning window and Fast Fourier Transform (FFT) are used to analyze the harmonic currents in the frequency domain, and to determine the spectral distribution of the harmonic currents and total harmonic distortion (THD). Finally, the range of possible fluctuations in harmonic amplitude is given by the method of statistical analysis of confidence intervals, and the harmonic limits are analyzed and verified against industry standards. The work in this paper is expected to provide a certain reference value for the design of permanent magnet motors and the protection of track circuits.