Due to the access of overhead ground wires of different voltage level transmission lines, the topology structure of the main grounding grid of substation operating with overhead ground wire will change significantly, and its grounding impedance cannot be measured by simply using the grounding impedance measurement method of power system grounding device. Moreover, it’s usually hard to unlock the overhead ground wire and measure the substation grounding impedance in operation, and the measurement will inevitably be affected by the diversion of overhead grounding wire. In order to eliminate the influence of overhead ground wire, it is required to measure the shunting current of each outlet frame connected with the overhead ground wire. In this paper, a grounding impedance measurement test for the main grounding grid of a substation operating with overhead ground wire is carried out, and a method of measuring the overhead ground wire shunt based on flexible Rogowski coil and frequency selective multimeter is proposed. The results show that the overhead ground wire diversion ratio can reach 43.4%, and the angle between the shunt current and the class power frequency current injected into the main grounding grid as a reference is -19.5°. The grounding impedance of the main grounding grid of the substation is calculated, and the error between the calculated result and the experimental result is very small. The results demonstrate that the measurement method of grounding impedance of substation with overhead ground wire and the measurement method of overhead ground wire shunting are correct.