Based on the non-oriental Super-SBM Model and Malmquist Index, this paper develops a comprehensive performance evaluation index for teaching and research in universities and proposes a methodology for performance evaluation. It also presents an in-depth analysis of the operational performance, both dynamically and statistically, of S University and its colleges and schools based on data from 2012 to 2015. This would provide a basis for decision making during resource allocation scientifically, and stimulate its internal motivation and development vitality to build a leading world-class university. Empirical research revealed that the performance level of teaching and research in S University was relatively high in 2015 and most colleges and schools showed valid performance appraisal, while four colleges and schools required reasonable resource allocation. For the four years from 2012 to 2015, S University maintained a good position in its teaching and research performance with no obvious distinction seen among its different colleges and schools, and with economies of scale prevailing in the teaching and research performance of its colleges. However, a slow decline in the total factor productivity index was seen in this period. Nevertheless, the findings revealed that the comprehensive performance of a university is mainly dependent on the management.