The Variational Mode Decomposition(VMD)method is introduced into the GPR signal processing. According to the non-stationary characteristic of GPR signal, the method of signal de-noising based on VMD principle has been established. The VMD is used to decompose the radar wave signal into the intrinsic mode function(IMF), and then the entropy of sample is used to determine whether the higher-order IMF is reserved to remove the noise. The accuracy and validity of the method are verified by GPR with Ricker wavelet and forward model test of de-noising, and the proposed method is compared with the traditional wavelet transform and the EEMD(ensemble empirical mode decomposition)method. After that, this method is used to analyze the GPR signal of a practical engineering. The results show that the method can effectively remove the noise in the GPR data and can obtain above 20 dB signal-to-noise ratio(SNR)even under strong background.