Abstract:The paper conducts the research on the High-Tech industries innovation efficiency in Yangtze River Delta and Pearl River Delta region from 2003 to 2012 based on the DEA-Malmquist model, and decomposes the TFP growth into two parts, which is technical change and technical efficiency change. Conclusions show that the High-Tech Industry Innovation Efficiency in Yangtze River Delta and Pearl River Delta region is growing as a whole, and the TFP growth is mainly from technical progress, and presents an unstable trend; while total factor productivity in Pearl River Delta region is significantly higher than in Yangtze River Delta region, and scale efficiency is no significant growth in the two regions, thus the two regions should not only improve technology but also need to achieve optimal allocation of resources.