The extraction of single train signal is necessary in wayside fault diagnosis because the acoustic signal acquired by a microphone is composed of multiple train bearing signals and noises. However, the Doppler distortion in the signal acquired by a microphone effectively hinders the signal separation and fault diagnosis. To address this issue, we propose a novel method based on the generalized S-transform, morphological filtering, and time–frequency amplitude matching-based resampling time series for multiple-Doppler-acoustic-source signal separation and correction. First, the original time–frequency distribution is constructed by applying generalized S-transform to the raw signal acquired by a microphone. Based on a morphological filter, several time–frequency distributions corresponding to different single source Doppler fault signals are extracted from the original time–frequency distribution. Subsequently, the time–frequency distributions are reverted to time signals by inverse generalized S-transform. Then, a resampling time series is built by time–frequency amplitude matching to obtain the correct signals without Doppler distortion. Finally, the bearing fault is diagnosed by the envelope spectrum of the correction signal. The effectiveness of this method is verified by simulated and practical signals.