Abstract: Scientific research efficiency is an important index of the ability of an institution to comprehensively utilize scientific research resources, especially in "Double First-Class" Universities in China. It is significant for guiding the optimal allocation of universities’ scientific research resources as they are constructed. In this study, an evaluation index system for "Double First-Class" Universities’ scientific research efficiency is constructed based on the characteristics of their scientific research activities. Their efficiency is evaluated scientifically through an output-oriented two-stage super efficiency Data Envelopment Analysis model, and key influencing factors of efficiency are identified using the improved Grey Correlation Analysis method. 27 "Double First-Class" Universities’ scientific research efficiencies are calculated based on data from 2016 to 2018. The results show that: (1) The two-stage DEA model considers the hysteresis of scientific activities and can calculate the decomposed efficiency. (2) The overall scientific research efficiency of "Double First-Class" Universities in China is low, and there is a wide range of efficiencies among the universities. (3) Number of highly cited papers and the total number of published papers are the key influencing factors of scientific research efficiency. Based on these results, some suggestions are put forward to improve the scientific research efficiency of "Double First-Class" Universities in China.