The phenomenon of Doppler distortion in the acoustic signal of moving acoustic source acquired with a microphone leads to the difficulty for signal analysis. In this paper, a Doppler distortion removal method based on energy centrobaric method is proposed to solve this problem, and applied in the fault diagnosis of train bearings. Firstly, the instantaneous frequency (IF) estimation (IFE) based on energy centrobaric method is applied to attain the IF vector. According to the Morse acoustic theory, the data fitting is then carried out to achieve the fitting IFs with which the re-sampling sequence can be established as the re-sampling vector in time domain. Through the resample, the Doppler distortion effect could be removed. Finally, a simulation and an experiment with practical acoustic signals of train bearings with a defect on the outer race and the inner race had been carried out in this paper, and the results verified the effectiveness of this method.