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Aiming at the problems of lack of diagnostic knowledge, low diagnostic efficiency and bad sharing of complicated aviation equipment, an example of infrared missile is taken and an intelligent fault diagnosis method of missiles based on OWL ontology and SWRL rules is put forward. Firstly, FMECA results of the missile are regarded as knowledge source. The ontology model of the missile is constructed by OWL description language based on ATML grammar, which is used to realize the mapping between fault modes and fault causes ontology. Then semantic network rule language SWRL is adapted to describe rules of knowledge base, which builds the relationship among class, property and instance. Finally, Racer inference engine is used for fault diagnosis and reasoning of knowledge base, and fault diagnosis priority is received. Reasoning results show that this method can solve the problems of difficulty of knowledge representation, lack of auto semantic reasoning, bad sharing and reuse of complicated aviation equipment effectively. The best path of fault diagnosis is received and the steps of fault check is reduced, which realize the quick positioning of fault causes and improve expert system diagnosis efficiency and reliability of complicated aviation equipment.