Considering the rapid development of the unmanned aerial vehicle (UAV) industry, it is crucial to prevent UAVs from accidentally entering substations. Installation of anti-UAV equipment is the most effective way to address this issue. However, the influence of electromagnetic interference (EMI) signals emitted by anti-UAV equipment on time synchronization devices (TSDs) used in substations has not been investigated in detail. This paper proposes an EMI evaluation method for the effect of anti-UAV equipment on TSDs. Simulations and Experiments were conducted to validate the proposed method with the results indicating that deceptive anti-UAV equipment (DAE) is more suitable for substations than suppressive anti-UAV equipment (SAE). Moreover, it is established that DAE should be installed 60 m away from TSDs in substations. This recommendation offers valuable guidance for the installation and deployment of anti-UAV equipment in substations in the future.