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In this paper, a more subjective Synthesis Evaluation algorithm is studied, in which hierarchy of criteria is generated through analysing the internal structure of research data by using exploratory factor analysis, weights are determined by using confirmatory factor analysis and with the application of TFN, more reliable judgements and reasonable evaluation results will be acquired. Furthermore, a computer aided Fuzzy-AHP evaluation prototype with B/S structure applying the above algorithm is developed in Microsoft Visual Studio. Net 2005 environment through proposing a function model by employing IDEF0 and constructing a conceptual relation model of database by employing UML. The system is capable of putting into the hierarchy of criteria dynamically and enables experts to score a project through internet, which provides a fast way to solve the problems of fuzzy evaluation.