The angle of attack and sideslip angle are the key parameters that affect the safety of flight control system. However, it is difficult for the atmospheric data system to accurately measure the air flow angles in severe weather or highly maneuvering flight, and flight safety issue may occur in the case of fault isolation failure. Based on this, an Adaptive Unscented Kalman Filter (AUKF) based flow angle fusion method is proposed. The filtering model is constructed by the information of inertial navigation system and aircraft dynamics model. At the same time, the adaptive filtering idea is applied to AUKF, and the Chi-square test and adaptive fading matrix are constructed by using the observed residual sequence, and the high precision output of flow angle under dynamic flight and fault conditions is realized. The simulation results show that the performance of this algorithm is better than that of the traditional extended Kalman filter algorithm and it has great engineering application value.