In this paper, firstly, from the input-output perspective of technological innovation, technological innovation process is divided into technological development process and technological achievements transformation process. On this basis, technological innovation efficiency can be decomposed into technological development efficiency and technological transformation efficiency. Secondly, on the basis of the two-stage technological innovation, by analyzing each stage in the process of technological innovation input and output elements, we design the input-output index system in each stage respectively, and ultimately get the high-tech industrial technology innovation efficiency evaluation index system. Thirdly, we build a chain network DEA model to evaluate the two-stage process of technological innovation of high-tech industry, include the overall efficiency of technological innovation and the efficiency of the two sub-stages. Finally, use chain network DEA model to calculate the technology innovation efficiency, technological development efficiency and technological transformation efficiency of high-tech industry of China's 25 regions in 2000-2010. According to the calculation results of h the empirical analysis of the efficiency of technological innovation of China's high-tech industry, and provide a reference for the provision of policy advice.