Diesel engines are widely used in railway systems, particularly in freight trains. Despite their high efficiency in energy conversion, they usually generate high levels of acoustics pollution during operation. In order to mitigate this problem, a series of active/passive acoustics control methods are used to reduce noise. Most of these methods are only effective if the prior knowledge of sources is given. In other words, it is essential to recognize the acoustics source. Variational mode decomposition (VMD) is a signal processing method that enhances the signal corrupted by background noise. However, the decomposed results of VMD depend on their mode parameter and penalty parameter. Therefore, an evaluation method based on system modal parameters (natural frequency and damping ratio) is proposed to select the mode parameter, and the penalty parameter can be selected from the power spectra of signals. In order to increase the accuracy of decomposition for diesel engines and find out the sources of acoustics, a method combining VMD, fast independent component analysis, and Hilbert transformation (VMD-FastICA-HT) is proposed for the separation and identification of different sources for diesel engines. The optimization results indicate that when the penalty parameter value is 1.5 to 16 times the maximum signal amplitude, better decomposition results can be achieved. Therefore, the separated independent acoustics are more accurate in source identification. Furthermore, both simulation data and in situ operational data of diesel engines for vehicles are used to validate the effectiveness of the proposed method.