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In real life, because of the complexity of decision-making environment, traditional method of clustering analysis and decision making models have been unable to the solve problem effectively, which is needed to combine with other methods for comprehensive evaluation. This paper is based on SPA fuzzy clustering and DS-rough set analysis applied to Computer Culture Basis test system to help teacher make rational judgment with the achievements of student. First we describe the DS- rough set with the scores of students in the system and analysis the scores of 5 modules with SPA fuzzy clustering method, respectively. Finally it is convenient to develop a reasonable teaching program according to the clustering results.