Abstract: The development level of high-tech industry is related to the comprehensive competitiveness of a country or region. Scientific and effective evaluation of the innovation process efficiency of regional high-tech industry is of great significance to enhance the innovation ability of high-tech industry. This paper uses the three-stage chain relational network DEA model to measure the overall efficiency and three sub stage efficiency of high-tech industry innovation in China's provincial regions, and analyzes the correlation effectiveness between the sub stages of innovation system and the differences of regional innovation process efficiency. The overall efficiency and three-stage efficiency in China's high-tech industry have been improved to varying degrees, but on the whole, the value of innovation efficiency is not high, especially in the overall innovation efficiency and the efficiency of achievement transformation. Through the classification analysis of innovation efficiency, it is found that only a few regions have relatively high efficiency in the three stages of knowledge production, technology research and development and achievement transformation, which indicates that the innovation efficiency of most regions in China is not high. It is necessary to take corresponding measures to improve according to the low efficiency link in the innovation process.