Abstract:This paper uses the data on science and technology innovation in colleges and universities in 31 provinces of China from 2017-2021 as the basis of the study, and uses the BCC model and Malmquist index to carry out static and dynamic calculations on the efficiency of science and technology innovation in universities in different provinces, regions and city clusters. The results of the study show that: (1) The overall efficiency of science and technology innovation in universities in 31 provinces is relatively low, Science and technology innovation in universities have the problem of input redundancy in 17 provinces, output shortage in 29 provinces; (2) The efficiency of science and technology innovation in universities between regions is high in the west and low in the east; (3) The efficiency of university science and technology innovation among urban clusters shows the trend is Yangtze River Delta City Cluster > Chengdu-Chongqing Region Twin Cities Economic Circle > Yangtze River Economic Belt > Beijing-Tianjin-Hebei City Cluster. In order to improve the efficiency of scientific and technological innovation in universities, it is necessary to establish the strategy for allocating scientific and technological resources based on efficiency, the evaluation mechanism for innovative achievements take the aim of benefit and the service-based research policy system.