Very fast transient overvoltage (VFTO) will affect the normal and stable working state of the secondary equipment of the power system by cable transmission and space radiation. In order to evaluate the electromagnetic immunity and enhance the reliability of the secondary equipment of the power system, there is no doubt that it is important for us to accurately model the voltage waveform of the secondary side interference. In this paper, the electromagnetic interference voltage of potential transformer (PT) secondary side in common mode in 1000 kV GIS Substation is measured. Secondly, the time-frequency characteristics of the voltage waveform of the secondary side electromagnetic radiation interference were analyzed by the synchronous compression wavelet transform (SWT) method. On this basis, the secondary side interference model is proposed and the parameters of the model are extracted by employing the differential evolution algorithm (DE). It can support and improve the EMI filters design and the immunity generator design of secondary equipment under VFTO excitation, which can also promote the immunity standards setting and revising of secondary equipment in the future.