Abstract: Based on value chain perspective, the innovation process is divided into two interrelated stages of technology R&D and economic transformation. The stochastic frontier model is used to measure the R&D efficiency and economic transformation efficiency of 30 provincial high-tech industries in China during 2009-2015. Then this paper analyzes the influence of spatial effect and other factors on the two-stage efficiency. The empirical results show that there are great differences in the R&D efficiency and economic transformation efficiency of high-tech industries in various regions; the spatial effect has a significant positive impact on R&D efficiency and a significant negative effect on economic transformation efficiency; the firm size has a significant U type relationship with R&D efficiency and a significant positive correlation with economic transformation efficiency; government funding support has a significant negative impact on technology R&D efficiency, and government tax reduction can significantly promote economic transformation efficiency. Finally, according to the overall mean of the two-stage efficiency, various regions are divided into four categories, such as high R&D and high conversion, high R&D and low conversion, low R&D and high conversion, low R&D and low conversion.