Abstract:Based on the theory of input-output and performance evaluation, combined with the characteristics of scientific research innovation universities, the evaluation index system of scientific research innovation performance in universities is constructed. Using the DEA-Malmquist-Tobit model, the static and dynamic analysis and evaluation of the scientific and technological innovation performance of the 2008-2017 senior triangle universities were carried out; the influencing factors of the scientific research input and output performance were explored. The research results show that the performance level of scientific research innovation in the universities of the Yangtze River Delta is low, and the total factor productivity (Tfpch) is declining. Factors such as the policy environment, the degree of external relations, the structure of teachers" titles, and the input of regional economic strength have a significant impact on the performance of scientific research innovation in universities.On this basis, resource allocation strategy and external environment, this paper puts forward some policy suggestions to improve the performance of scientific research and innovation in universities across the Yangtze River Delta from the aspects of internal management system.