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Cognitive map is a graph model that expressing and reasoning the causal relationship between concepts in systems. Cognitive map reasoning is the process of reasoning the unknown knowledge by using the known knowledge with the help of cognitive map. In view of the lack of systematic research methods in terms of the cognitive map reasoning mechanisms currently, this paper analyzed the four key issues in the process of reasoning based on intensive study of cognitive map reasoning methods. That is the choice of transformation function, the determination of the times of iteration, the selection of reasoning model, and the judgement of the final state. Then this paper proposed a general algorithm of cognitive map reasoning based on matrix, and that is proved to be effective by an example.