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The modeling of fault diagnosis system is a difficult issue in the fuzzy Petri nets (FPN) fault diagnosis system. The method for generating FPN fault diagnosis model is proposed by using rough set theory. Firstly, the condition attribute and attribute value of swatch set of the faults is reduced by using the rough set theory, and the default rules are got by using Skowron default manner. Then calculate the condition weight of the default rules according to the credible degrees of knowledge in the rough set theory, and the fuzzy weighted production rule are got. And then analyze the conversion method of the fuzzy weighted production rule and FPN model. Finally, the FPN diagnosis model of a torpedo receiver subsystem is established, and experiment shows the feasibility and efficiency of the proposed method.