It is an important path to implement the performance based funding requirement of the "Double First-Class" policy by assessing the efficiency of research of universities,optimizing the allocation of research resources and improving its efficiency. This article selects the "Double First-Class" universities that directly under the Ministry of Education as a sample to assess the research efficiency and its changes of universities during 2010-2015. An indicator system which highlights the quality and contribution of scientific research is utilized,and DEA-BCC model and the Malmquist index are employed. The results show that:the overall research efficiency of these universities was low,slowly improving during the period,which was mainly enhanced by the increase in management efficiency and scale efficiency; however,the scale effect was decreasing. The research efficiency of universities in the central and western regions fluctuated significantly due to the unstable research funding,and the research efficiency of universities specialized in science and engineering (S&E) continued to decrease. In the future,it should depend more on the improvement of research management and technology innovation to increase research efficiency and get rid of the heavy dependence on the factor-driven model. Moreover,it should stabilize the investment and better the match between funds and human resources of the universities in the central and western regions,and optimize the disciplinary structure of the S&E universities.