The UAV positioning system is an important core module for the information interaction between the UAV and the external environment, it also provides a coupling path for electromagnetic interference signals. Based on the internal structure of the UAV positioning system, the interference sequence diagram of the UAV positioning system is established, then the transient response function of each module of the UAV positioning system is derived, the physical model of the UAV positioning system is constructed based on the interference sequence diagram, and the joint analysis of the electromagnetic effect field path of the positioning system is carried out. The distribution and law of the magnetic field strength H and magnetic induction intensity B of the positioning system and its sensitive unit are simulated and analyzed, and the electromagnetic effect distribution characteristics and electromagnetic weak links of the UAV positioning system are obtained. The simulation results show that the electromagnetic weak link of the UAV positioning system is at the connection point of the chip line, and with the increase of the electromagnetic pulse interference time, the electromagnetic effect continues to accumulate and shows a consistent trend of oscillation effect.