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Information system is a large-scale complex system. It includes many uncertain factors, as software, hardware, people and so on. As a result, information systems security risk is related to many ambiguous factors, what are difficult to measure, with ambiguity. This paper introduces the information system security risk generating mechanism, and based on the risk assessment of factors, builds information system security risk assessment model based on fuzzy analytic hierarchy process, which could be used to evaluate the security situation of information system.