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This paper focuses on the frequent faults of Component-based military software during the process of the software using, the uncertainty problems of traditional methods of rule-based reasoning for software fault diagnosis, and proposes the fault diagnosis method based on uncertain rule knowledge base. First, analyze the uncertain factors of traditional rule-based reasoning according to the logic of uncertain reasoning, and build the knowledge base of uncertain rules. Then, based on this knowledge base and the forward chain of reasoning strategies, calculate the uncertainty factor, legitimately set the threshold to activate rules, and sort the certainty factors of intermediate conclusions to eliminate conflicts. Experiment results show that, the military software fault diagnosis method based on uncertain reasoning has a higher accuracy rate compared with traditional accurate reasoning method. 