At present, Chinas cooperation among industry, universities and research institutions is still at the exploratory stage, and more often than not, it needs the governmental support to realize the reasonable allocation of resources. Based on the panel data of 2008—2017 in China, this paper constructs a SDM model based on the measurement of innovation efficiency of enterprises, universities and scientific research institutions, and empirically analyzes the spatial spillover effect of innovation efficiency of each subject and the role of government in the cooperation. The results show that: (1) among the three innovation subjects, the average innovation efficiency of universities is the highest, followed by enterprises, while that of scientific research institutions is the lowest; (2) the role of universities and scientific research institutions in promoting the innovation efficiency of enterprises has not been fully shown; (3) under the guidance and support of the government, both of them will significantly improve the innovation efficiency of enterprises, and there is a significant positive gap spillover effect. This conclusion will provide an important basis for the government to formulate the strategy of industryuniversityresearch institution cooperation.