Abstract Attitude Measurement System (AMS) that constructed by the low-cost Micro-Inertial Measurement Unit (MIMU) is usually adopted as the backup equipment for the fixed-wing Unmanned Aerial Vehicle (UAV) to enhance its safety performance during flight. However, both the large-maneuvering acceleration and the high-frequency propeller dithering are major reasons that decreasing its real-time measurement precision. In addition, there are only tri-axial gyroscope and tri-axial accelerometer measurements could be utilized to compensate the measurement errors in the autonomous MIMU based AMS. In this paper, an Adaptive Mahony Complementary Filter (AMCF) with dynamic tuning of the complementary filter Proportion and Integral (PI) parameters is used to estimate the real-time attitude of the highly dynamic aviation UAV with low-cost MIMU in high-frequency propeller dithering. Meanwhile, the maneuvering acceleration compensation technology is also integrated with the AMCF to eliminate the UAV highly dynamic maneuvering acceleration. Moreover, the attitude of AMS is updated by the quaternion updating algorithm to improve its real-time performance and reliability. Finally, both UAV ground high-speed taxiing experiment and UAV flight experiment are conducted to verify the measurement accuracy of low-cost AMS. The real-time flight experimental results demonstrated that the Rooted Mean Square Error (RMSE) of AMS based on the low-cost MIMU do not exceed 0.882° in terms of pitch angle and 0.864° in roll angle under various maneuvering conditions. These results provide powerful supports for both the UAV developers and the low-cost MIMU based AMS.