Based on the panel data of 31 provinces,municipalities and autonomous regions in China from 2015 to 2017,the DEA model is used to estimate the efficiency of scientific research in inter-provincial universities. Results show that the efficiency of scientific research in universities in different regions is generally low. Under "Double First-Class" construction,the overall efficiency of scientific research shows an increasing trend. The efficiency of scientific research in western universities is relatively high,followed by the universities in central and eastern regions. Then the Tobit model is used to analyze the factors that affecting the efficiency of scientific research in universities. It is found that the investment of human capital in universities is in a state of "scarcity" and material capital is in the state of "redundance". Scientific research institutions have such problem as focusing on quantity but not on quality. The connotative development of universities in China should focus on the accumulation of human capital and reduce the excessive investment of material capital,strengthen international exchanges and cooperation,and make great efforts to promote the construction of "Double First-Class",to improve the efficiency of scientific research in universities and to enhance the international discourse right of universities in China.