Abstract:the improvement of basic scientific research innovation efficiency of scientific research institutions is of great significance to the construction of an innovative country in China. In view of this, on the basis of considering the characteristics of basic scientific research of scientific research institutions, this paper uses the super efficiency DEA method to evaluate the current situation of basic scientific research innovation efficiency of scientific research institutions in 31 provinces and cities of China in 2009-2017, and further studies human capital from two dimensions of the whole country and regions by taking the evaluation value of basic scientific research innovation efficiency of scientific research institutions as the explanatory variable and combining the GMM model of the system The impact of economic development, opening up, industrial innovation and foreign investment environment on the efficiency of basic scientific research innovation of scientific research institutions. The results show that the basic scientific research efficiency of scientific research institutions in China is generally low, and it is decreasing from east to west. In terms of the whole country and regions, the basic scientific research innovation efficiency of scientific research institutions has cumulative effect, and the changes of human capital, economic development, opening up, industrial innovation and foreign investment environment will have different effects on the improvement of basic scientific research innovation efficiency of scientific research institutions There are regional differences in the influence. In order to improve the basic research efficiency of scientific research institutions in China, it is necessary to adopt strategies such as improving the investment mode of innovative resources, optimizing the structure of innovative human capital and expanding the degree of academic exchange and opening up of scientific research institutions.