This paper examined the research efficiency of Chinese higher education institutions with a sample of 105 universities (35 universities in each group of "Project 211", "Project 985" and general universities). In order to analyze the relative research efficiency among "Project 211" and "Project 985" and general universities, the method of Data Envelopment Analysis (DEA) was implemented with EnPAS software. The result showed that research efficiency of "Project 211" universities was lower than "Project 985" and general universities. Secondly, the research efficiency of the selected universities in China differed by region (eastern, central, western) and the type of universities (polytechnic, comprehensive, others). The implications of this study were presented at the government and university levels. The government should rearrange the financial support programs and evaluation criteria for universities. Universities also need to formulate strategies and systems for efficient operation and performance improvement.