Lightning protection near the fan is the key point of lightning protection in wind farm, which affects the safe and effective delivery of wind power resources. At present, the three-phase multi-gap arrester installed on a base tower behind the collector can cooperate with the zinc oxide arrester to reduce the system failure caused by the arrester failure. However, the chopped wave generated by the multi-gap arrester when it acts is transmitted to the fan box transformer along the line, which may threaten the insulation of the transformer winding. Based on the above problems, this paper builds a simulation model on ATP to analyze the impact of wave clipping of multi-gap arrester on the insulation of fan transformer windings, considers the conventional installation mode and the limit installation mode of multi-gap arrester, and calculates that the wave clipping overvoltage generated by multi-gap arrester after being struck by lightning in two cases is the impact on the insulation of fan transformer. Through the simulation analysis, it is found that the higher the amplitude of the lightning current, the larger the amplitude of the overvoltage generated by the truncated wave, the steeper the wave head, and the greater the threat to the insulation of the fan box. The damage degree of round lightning is less than that of counter lightning. When a multi-gap arrester is installed in a collector tower, the 100[Formula: see text]kA lightning current may destroy the insulation of the fan box transformer winding and require additional protective measures. It is recommended that the multi-gap arrester be installed from the next pole tower of the collector tower in the wind farm.