As the main factor of China’s higher education, effective evaluation of the scientific research efficiency of domestic universities is extremely significant to improve the scientific research management system of local universities, optimize the allocation of scientific research resources, and promote regional economic development. Based on the ten-year statistical data of the compilation of science and technology statistics of colleges and universities, this paper adopts the data envelopment analysis (DEA) model to study the scientific research efficiency of 31 provincial universities in Shandong Province from three dimensions: level, type, and region. The results show that, first, the overall scientific research efficiency of the sample universities is not high and takes on a downward trend; there are some differences, changes in the same direction, and level convergence in each dimension of scientific research efficiency. Second, there is a positive correlation between the comprehensive scientific research strength of the sample universities and the technical efficiency. Third, the level of regional economic development has a positive impact on the scale efficiency of scientific research, which is closely related to the technical efficiency, and there is no positive correlation between these two. Thus, the research suggests that, in the future, colleges and universities should formulate differentiated management policies, build a “Government University” two-level scientific research performance evaluation system guided by scientific research quality, change the concept of scientific research managers, and improve the ability of personnel to improve the efficiency of scientific research in colleges and universities.
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