Positioning system is the electromagnetic sensitive part in the core unit of unmanned aerial vehicle (UAV) and the key part of UAV electromagnetic protection. To analyze the failure process and mechanism of electromagnetic interference, aiming at the positioning system of typical self-assembled UAV, the radiation coupling path is analyzed by constructing the electromagnetic topology and the radiation interference effects of different coupling paths of UAV positioning system are simulated and analyzed. The GPS enhanced forwarding system is used to provide a normal working environment for the UAV system in the anechoic chamber and the microwave irradiation interference effect experiment is carried out. Through the logging function in the UAV’s firmware, combined with the real-time monitoring data in ground station, the whole process data recording and fault mechanism analysis of the electromagnetic interference of the UAV positioning system are realized. The experimental results show that the coupling interference of the receiving antenna mainly occurs within the maximum receiving bandwidth (200 MHz) of the positioning system; Cable coupling interference mainly occurs in the frequency band below 1 GHz and reaches the maximum near 171 MHz and 511 MHz; The coupling interference of PCB circuit mainly occurs in the frequency band above 1.24 GHz and the fluctuation of coupling voltage becomes stronger with the increase of interference signal frequency.