Accordingly to the problem that during the fault diagnosis of the flap system, the existing experience and knowledge are always uncertainty, inconsistency, incompleteness, what’s more, the different fault cause has different effect on the fault. So the Weighted Fuzzy Petri Net is adopted, and fuzzy Petri net and matrix operations are combined, then the formal process of fuzzy inference reasoning algorithm is researched in order to obtain the fault probability of each event in the fault tree of flap system. The presented method effectively makes up the deficiency of the traditional FTA and FMEA, and provides a new fault diagnosis method for complex systems, so the fault diagnosis method based on Weighted Fuzzy Petri Net has a great practical value.