Targeted at the faults of autopilot in fly-by-wire flight control system, a method based on integration of case and fault tree is proposed to quickly diagnose faults and provide the maintenance of autopilot system. In the process of diagnosis, according to the characteristics of fault information about autopilot system, the Build-in-test data was used to quickly search similar fault in the case base and accurately point out the fault location. For complex fault, the fault tree method is used to traverse to complete the reasoning and diagnosis procedure, and simultaneously add the results to the case base. The simulation results show the method is achieved.