The disconnector operation in the high-voltage substations forms a very fast transient overvoltage (VFTO), which leads to a sudden rise in local grounding potential. Due to double grounding of the secondary cable, the current transformer signal is interfered by the grounding grid potential difference. To study the mechanism of the interference signal, a simulation model based on the electro-magnetic transient program is built and the coupling path of the grounding grid potential difference is analyzed. According to the characteristics of interference signal, an adaptive algorithm is put forward and it mainly consists of three parts, including starting element, decision algorithm, and filtering algorithm. By selecting the appropriate parameters of wavelet transform, the filtering algorithm can discompose and reconstruct signal to remove the interference signal. The simulation results demonstrate that the filtering algorithm can effectively eliminate the interference signal caused by the grounding grid potential difference, with a 91% reduction of the root mean square error and a 135% improvement of the signal-to-noise ratio. Moreover, the accuracy of the measured data is ensured and the reliability of the relay protection is improved.