Rough set theory is another mathematical tool for dealing with uncertainty after probability theory, fuzzy set, and evidence theory. As a newer soft computing method, rough sets have received more and more attention in recent years. Its effectiveness has been confirmed in many successful applications in science and engineering fields. It is currently the leading technology in artificial intelligence theory and its application in the world. One of the research hot spots. This article systematically studies the ideas and methods of constructing and optimizing each index system in performance appraisal, solves the difficult problems in the construction of the index system and evaluates the quality of the index system construction, and systematically applies rough set theory to the whole process of comprehensive evaluation. In this method, rough set theory and comprehensive evaluation theory are combined to better solve difficult problems in the comprehensive evaluation process.