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As the knowledge in the fault diagnosis of civil aircraft is dynamic and uncertain, a method based on the Adaptive Fuzzy Petri Net(APFN) is proposed to solve the problem. AFPN not only takes the descriptive advantages of fuzzy Petri net, but also has learning ability like neural network. By this mean, firstly set up a fuzzy Petri net using the fuzzy production rule. Then the parameters of the fuzzy Petri net are trained by BP learning algorithm. At last, when the weights of the fuzzy Petri net are fixed, the fault origin can be found through the fault inference. At the end of the paper, an experiment is designed to demonstrate that the approach is feasible and effective in fuzzy reasoning.