Abstract: In order to test the safety and reliability of the Unmanned Aerial vehicle (UAV) system under the environment of lightning pulse magnetic field, a certain type of UAV was regarded as the test object. Lightning pulse magnetic field was simulated using the Helmholtz coil and the lightning surge generator. The experimental result shows that the lightning pulse magnetic field of 8/20 s as recommended in the national standard GB50057-94 does not interfere with communication to cause the data link unlock. But three axial magnetic heading sensor is interfered seriously to produce drift and cause reading deviation on known direction. Besides, the polarity of discharge determines variation trend of course angle. After a thorough analysis of mechanism, the magnetic heading sensor can work normally in the linear area by using anisotropic magneto resistance effects regularly changing the resistance value. But the high peak value lightning pulse magnetic field will lead to permalloy resistances disordered arrangement of internal magnetic domain and magnetization, which changes the magnetic sensitivity of sensor and output characteristic, and only appears on the magnetic sensitive direction.