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In the current evaluation model of information system, different field information systems are evaluated by standardized evaluation attributes, which can not meet quality for information system. In the paper the new evaluation mode is proposed which supports to customize evaluation attributes dynamically, and new TFAHP which has fuzzy evaluation adjustment attribute is also proposed, and approach of fuzzy comprehensive evaluation is improved. At the same time based on combination of them, a new algorithm model to suit modern information system is created. The prototype is designed, which is applied to project case evaluation fruitfully, and the experiment results are veracious and reliable as well as stable.