The study takes 10 urban agglomerations in China as the research object, focusing on the Chengdu-Chongqing urban agglomeration, and applies Data Envelopment Analysis (DEA) to measure and compare their scientific input and output efficiency of universities. First, this paper analyzes the input and output of scientific research in universities in major provinces in China in detail. Second, according to the construction principles of the indicator system, using qualitative interview to construct evaluation indicators of university research efficiency. Third, using DEA method, first analyze the input and output profile of some urban agglomeration universities such as Chengdu-Chongqing economic circle, measure and compare their research input and output efficiency, then compare and analyze the research efficiency of research-type sample universities within Chengdu-Chongqing economic circle, and conduct a projection study of non-DEA effective sample universities. The main conclusions are as follows: first, the average efficiency of scientific research in universities in Chengdu-Chongqing and other urban agglomerations in 2020 has slightly increased compared with that in 2016, but the gap between urban agglomerations is prominent, and the innovation level of scientific research in higher education institutions in urban agglomerations needs to be improved. Second, there is a mismatch between the themes of research, funding and human resources in research-oriented universities in the Chengdu-Chongqing economic circle. Third, there is considerable room for improvement in research efficiency, and the influence of scale on overall efficiency is weak. We found that excessive investment in scientific research in universities is the main reason for the non-effect.