Abstract: Based on a two-stage chain perspective, this study divides the innovation system of China’s high-tech industry into R & D systems and technology and the transformation of systems, and uses multi-stage high-tech super-efficiency DEA to estimate the efficiency of industrial innovation systems and two sub-level of development. Based on the model of coordinated development, the synergies of the two subsystems are calculated by its evaluation of synergy, and we find that the overall system of innovation and high-tech industry in China’s synergy is low, and the industry has shown significant differences and disparities, but the main source of R & D efficiency is poor. Based on the development level of the two systems, 17 sub-areas are be divided into four sub-sectors, and in-depth analysis of their characteristics and reasons for different types of the corresponding policy recommendations are put forward.