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In view of the problem that there are more fuzziness and uncertainty in the fault diagnosis (FD) of bus of integrated ship electronic system and it is hard to achieve FD rapidly,this paper proposed a new approach of FD for bus of integrated ship electronic system by adaptive fuzzy petri net (AFPN).On the basis of weighted fuzzy petri net(WFPN), neural network technology is introduced and the formalize definition and learning algorithm of AFPN are given. A case study of BN is given to verify the proposed approach. The case study shows that the AFPN model has good adaptive ability and reasoning ability, avoiding the uncertainty and contingency coming from personnel experience. The proposed approach can achieve FD of bus of integrated ship electronic system rapidly and accurately.