The automatic flight control system has complex structure with many relevant components, resulting in long time fault diagnosis, which affects the efficiency of aircraft operation. Aiming at the problems, a remote real-time fault diagnosis scheme based on Aircraft Communication Addressing & Reporting System (ACARS) was proposed. Firstly, the fault characteristics of the automatic flight control system were analyzed, and the detection filter was designed and built. Then, the key information of the automatic flight control system transmitted in real time by ACARS data-link was used to realize the residual calculation of the relevant components, and the fault diagnosis and location were carried out according to the residual decision algorithm. Finally, because of the large difference between residual errors of different fault components and inconsistent decision-making threshold, an improved residual decision-making algorithm based on quadratic difference was proposed. This algorithm reduced the overall change trend of the detection object, reduced the influence of random noise and interference, and avoided a transient fault being considered as a system fault. The simulation results show that the proposed algorithm avoids the complexity of multiple decision-making thresholds. Its fault detection time is about 2 seconds with 0.1 second sampling time, which shortens the fault detection time greatly, and the effective fault detection rate is more than 90%.