Abstract: R&D innovation activities in high-tech industry can be divided into two stages of technology development and achievements transformation from the point view of value chains. This paper measured the R&D activities two-stage total factor productivity of high-tech industry based on provincial panel data from 1996 to 2010 by using Malmquist index analysis method from the point view of value chains, and at the same time examined the reasons, the direction and trends in productivity’s changing. The results show that the TFP in technology development stage rises significantly, average annual growth reaches 21.8%, and technical progress is the major driver of TFP’s growth rather than technical efficiency in this stage. But in the transformation stage, technical progress efficiency is decreasing, while technical efficiency is increasing. The eventual result is a slight decline in TFP, and average decrease rate reaches 0.9%. At last, some suggestions are given to improve R&D TFP of high-tech industry in China, such as developing preferential policies and incentives, changing technology development model, encouraging inventions, and funding promising products.