The substation line is usually located in the high-voltage area of the system. Although the general lightning protection reform measures for it will strengthen the lightning resistance level of the line and improve the operation reliability, they will also increase the lightning intrusion wave of the substation, which will have an impact on the insulation coordination of the equipment in the station to a certain extent, especially affecting the characteristics of the lightning arrester, resulting in the increase of overcurrent and heat, and then shortening its service life. In summary, taking a 330 kV substation and its line segment in a high-altitude area as an example, ATP-EMTP (the Alternative Transients Program—the Alternative Transients Program) was used to establish a simulation model, and the influences of different poles and towers in the line segment on the current and overvoltage of the arrester in the station were, respectively, explored. Based on this, considering the condition of the line body and the insulation cooperation with the equipment in the station, the differentiated lightning protection transformation of the line segment is finally realized.