As a key equipment of the high-speed Electric multiple unit (EMU), the Balise transmission module (BTM) is tend to be affected by electromagnetic disturbances. However, the existing filter can not well eliminate electromagnetic disturbances. In order to improve the Signal to noise ratio (SNR) of BTM uplink signal, Variational mode decomposition (VMD) method is introduced into de-noising the uplink signal polluted by disturbance. The proposed de-noising method decomposes the noise-polluted signal into several narrow band sub-signals. And then, the de-noised BTM transmitting signal is reconstructed by the sub-signals of the same frequency as the BTM carrier. To improve the accuracy of the VMD based signal decomposition, the Normalized short time fourier transform-Wigner ville distribution (NSTFT-WVD) method are applied to determine the decomposition mode number of the target signal. The proposed method is used to deal with both simulation signal and measured BTM uplink signal. Results demonstrated good improvement in SNR by 20dB and 12.63dB, respectively.