We established a model based on the ''Malmquist index'' to evaluate the dynamic performance of scientific and technological innovation in seven Chinese universities, which included five categories: changes in pure technical efficiency, changes in production technology, changes in scale efficiency, changes in organizational management performance, and changes in comprehensive efficiency. Seven domestic firstclass universities were studied, and empirical analysis was performed based on data related to their scientific and technological innovation during three time periods (2013-2014, 2014-2015, and 2015-2016). Our results demonstrated that the contribution rate for each index was different for each university across the three time periods, and that Chinese universities is gradually transitioning from resource allocation to technical efficiency. In this paper, we explored the transformation from effect to efficiency and static to dynamic in the evaluation of the scientific and technological output of colleges and universities, and constructed systematic and unique multi-evaluation system for the scientific and technological output of universities.INDEX TERMS Dynamic performance, university science and technology, data envelopment analysis, enhanced Russell measure, Malmquist index.