Abstract: According to the requirements of “essential demand of information system security level protection” to third class system, the paper built the evaluation index system of information security level protection for third class system, further analyzed the evaluation index, made the personnel evaluate the standard compliance of information system with pertinence. According to the index system of decomposition, the weight of index in the System was determined by analytic hierarchy process and subjective estimate method, the integrated evaluation results were got more precise. It was provided reference for the evaluation work.