Magneto-inertial navigation system (MINS) is widely used in navigation control of unmanned aerial vehicle. It can provide attitude and heading information via data fusion of accelerometer, magnetometer and gyroscope. Complementary filter is a concise and efficient solution for data fusion in frequency domain. Therefore, it is also called attitude and heading reference system (AHRS). A generalized complementary filter (GCF) is introduced to consolidate various complementary attitude filters that based on different transfer functions and orientation representations. In this paper, the multiplicative attitude error of this kind of algorithm is analyzed, and compensation algorithm for motional acceleration is also proposed, in order to enhance attitude accuracy under dynamic condition. Numerical simulation and experiment results show that GCF can achieve the same performance of extended Kalman filter, but its execution time is approximately 1 / 20 of the latter's. Moreover, GCF has ideal numerical stability, and it can eliminate the impacts of linear acceleration with the proposed motion compensation algorithm. Therefore, it is suitable for miniature and low-cost UAV applications.