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Currently, in the evaluation of excellent courses in colleges in our country has already formatted a specialized of nation excellent courses evaluation system. From 2003 the nation evaluation system of excellent course started beginning, with the gradually development and abundance also promote the construction of excellent courses in colleges. Therefore, this paper is set from the current excellent course evaluation system, with the combination of rough set and fuzzy AHP method to make a comprehensive evaluation to the excellent courses of Wenzhou University. This paper through the process of establish the model of rough set-fuzzy analytic hierarchy process (FAHP), the main idea is to pass the weight determination method of rough set theory to centralize the each index weight of one class, also take the foundation which through the combination of subjective weight and objective weight to carry on fuzzy comprehensive evaluation analysis. Pass the establishment of the excellent courses model in colleges to put forward a new kind of evaluation method.