Most radar stations are located in high-thunderstorm environment, and their power system is vulnerable to lightning strikes. Aimed at the problem of lightning protection in power system of radar station, the integrated protection of three-level surge protector and isolation transformer is adopted. Firstly, three-level Surge Protection Device (SPD) is used to reduce the amplitude of lightning current rapidly, then the isolation transformer is used to completely isolate the electromagnetic pulse energy and eliminate the residual voltage of lightning current, so as to achieve the protective effect. Through modeling, simulation and actual test, it can be found that the integrated lightning protection system has good protective effect on the impact of lightning current, can guarantee the normal power supply of the power system of radar station under the lightning environment, and can ensure the safety of radar equipment and operators. This work is supported by Army Scientific Research Project (No. ZBBG415238GT).