Attitude and heading reference system（AHRS）is an important instrument used to measure，calculate and provide flight attitude and heading information. Its indication accuracy directly affects the pilot's control and the performance of autopilot. Aiming at the fault that the magnetic heading error of a certain type of heading and attitude reference system is too large in the test process，in this paper，the mechanism of the system is theoretically analyzed，the fault tree is established，and the bottom events are analyzed one by one through actual operation detection，so as to screen the cause of the problem，and successfully locate and eliminate the fault. The results show that：the reason of the large magnetic heading error of the AHRS is that the meaning of the variables is confused when the GPS signal is used to correct the output value. The design of the magnetic heading algorithm is not rigorous enough，which leads to large error. The fault tree analysis method can successfully locate and check the fault.