The paper applies the three-stage network DEA and DEA-Malmquist method to measure the innovation efficiency of the high-tech Manufacturing industry for the period 2009–2017 in China. The analysis is divided into two parts to study. In the first analysis, we analyse the innovation efficiency of the high-tech manufacturing industry by using a three-stage network DEA, to open the black box of high technology innovation process in Chia. In the second stage, we use the DEA-Malmquist index method to evaluate the efficiency of technological innovation dynamically. We first found that the average innovation efficiency in the three stages from 2009 to 2017 shows a ‘Λ’ trend, there is room for improvement, especially in the basic and applied innovation stages. Moreover, the innovation is mainly driven by the east. Through the years 2009–2017, the development of high technology is unbalanced as well as insufficient. Our analyses show that the efficiency of technological innovation has been affected by the SEC and national policies. Therefore, we should adopt strategic measures to improve the innovation efficiency.