| Summary: | Higher education institutions (HEIs) are the key to the economic and social development of a country. However, the recent advancements of higher education institutions’ universities in China have become a pivotal factor contributing to their swift growth. Considering the impact of the external environment, applying a three-stage data-envelopment analysis (DEA) and the Malmquist index method, we evaluated the static and dynamic efficiency of input–output data of scientific research produced by universities directly under the Ministry of Education in the period of 2010 to 2017. Results showed that the three stage DEA model is more accurate than the traditional DEA method for measuring the efficiency of scientific research input and universities’ output. The overall efficiency of universities’ scientific research activities increased at an average annual rate of 3.7% from 2010 to 2017. Further analysis showed that the optimization of the scale was the primary internal factor able to promote the efficiency of scientific research in universities. Technological progress slightly diminishes the efficiency of scientific research in universities, which should, therefore, take measures to improve pure technical efficiency to enlarge the scale of their scientific research according to the characteristics of scientific research efficiency. Such steps will strengthen internal motivation towards scientific research efficiency in universities.
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