With the continuous improvement of substation voltage level and the wide use of GAS insulated SWITCHGEAR (GIS), switching overvoltage, especially the very fast transient overvoltage (VFTO) caused by disconnector operation, has attracted more and more attention. According to the demonstration project of a new generation intelligent substation with the highest voltage grade (330kV) in operation in China, analysing the physical process of VFTO generation and propagation in high voltage substation by combining simulation calculation with test detection. Taking the electronic current transformer of intelligent secondary equipment as an example, its exploitation is established. We got the output signal waveform of the acquisition unit port under the action of VFTO by the high frequency transient model of the unit. By comparing the distribution parameters and the measured signal waveforms, the high frequency characteristics of the acquisition unit of the electronic current transformer under the action of VFTO are reflected. The results show that the EMI of the acquisition unit of electronic current transformer is in the form of pulse group. The amplitude of EMI is about 900V and the stable impact frequency is about 50 kHz. The impact frequency directly related to the arc reburning frequency.