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Along with information network era widely accepted, the safety of information system faces a challenge and it is also seems to be necessity to evaluate its security risk. According to fuzzy comprehensive judgment theories, this text analysis the risk factors the information system involves from system risk, network risk, security management system, environment, and operation, and establishes the index system of information system security risk evaluation. It gives the evaluation method of information system security risk based on fuzzy comprehensive adjudicate. The model and method has been proved useful and effective by actual example.