The unbalanced traction current and the frequency shift signal of the ZPW2000 series track circuit have a common transmission channel. The traction returns and higher harmonic components will affect the frequency shift signal. When the train relies on the CTCS- 2 train operation control system to provide operation permission, increasing the risk of safe operation. In order to effectively remove highorder harmonic interference and obtain jointless track circuit frequency shift information, a frequency shift signal processing method based on the combination of VMD and Hilbert transform is designed. First, use VMD to decompose the harmonic interference signal into several IMFs of different frequency bands, solve the center frequency of all IMFs, determine the interference frequencies of each harmonic, and determine the eigenmode function corresponding to the current jointless track circuit according to the prediction algorithm and correlation verification; finally, determine the current jointless track circuit mid-shift by performing Hilbert transform analysis on the IMF Frequency information. Through the analysis of simulation and laboratory measured signals, it is found that the method not only effectively suppresses the mode aliasing phenomenon to make the harmonic interference components accurately separate from the mixed signals, but also accurately solves the frequency shift information, which provides a reference for the accurate demodulation of driving permit signals under interference conditions.