Abstract: High power electromagnetic pulse interference and even destruction of unmanned aerial vehicles is a very effective way to deal with the threat of small unmanned aerial vehicles (UAVs).The interference and damage of high power electromagnetic pulse to UAV system is mainly through the way of front door coupling and back door coupling. In this study, the damage of UAVs by high power electromagnetic pulse are analyzed, and the target vulnerability of UAVs under the electromagnetic pulse source is analyzed. According to the damage effect, the damage level of the high frequency electromagnetic pulse to UAVs is divided into three levels, namely the interference level, the damage level and the failure level, and the main targets of electromagnetic pulse are analyzed. The results show that the most vulnerable parts of the UAVs are the receiver and the electronic governor. Therefore, in future research and practical application, it is necessary to study the damage and destruction of the electromagnetic pulse to the receiver and the electronic governor. And the optimum frequency of damage should be determined based on the circuit configurations of the receiver and the electronic governor.