Based on Data Envelopment Analysis (DEA) models, such as CCR and BCC, considering the change of evaluation indicators for scientific and technology achievements, a comparative analysis on Universities’ R&D efficiencies and catch-up effect in 30 provinces of China during the period of 1999-2002 and 2003-2006 is conducted, and then the trend and stability of R&D efficiencies are studied by using DEA window analysis. At last, on the basis of window analysis results, an in-depth correlation analysis is discussed. The results show that R&D relative outputs, especially R&D relative outputs per capita, have an positive correlation relation with R&D efficiencies to a certain degree. By determining scientific and reasonable R&D output indicators, the focus is shifted from absolute R&D quantity outputs to relative R&D quality outputs, the R&D incentive system is improved and research staffs’ enthusiasm is boosted, and R&D funds and projects are rationally allocated. All of that can enhance the Universities’ R&D efficiencies in different provinces of China.