Abstract: With the gradually increasing R&D input of “985 universities”, the R&D performance of these universities becomes the focus. How to evaluate the R&D efficiency effectively is an important issue. Based on the panel data of 2006-2009, this paper selects the R&D personnel, R&D funding, expenditure of R&D projects as the input indicators and monography, published paper, outcomes transformed, results awarded as output indicators, and uses DEA and Malmquist index methods to evaluate the research efficiency of “985 universities”. The results show that overall research efficiencies of the “985 universities” are low, and from 2006 to 2009 the R&D efficiencies failed to progress significantly. Further analysis finds out that technological progress is the main factor that hinders the overall efficiencies. “985 universities” should promote the technological innovation and progress to improve the efficiencies of universities R&D