Abstract: The paper builds a two-stage dynamic DEA model from the perspective of the innovation value chain, and employs the model to analyze the R & D efficiency, export transformation efficiency, comprehensive efficiency and intertemporal dynamic change on the basis of 52 national high-tech parks panel data in China over the period of 2006-2017. The influencing factors are also analyzed by regression simultaneously. The results show that the average R & D , export transformation, and comprehensive efficiency of these areas show an upward trend in fluctuation as a whole, and the average value of the export transformation efficiency is the lowest among the three. In addition, the economic development and talent number of high-tech zones have a significant positive impact on the R & D innovation efficiency, the opening degree,debt financing, and the R & D innovation efficiency of these cities play a clear positive role for the export transformation efficiency, and geographic distance brings a noticeable negative effect on the export transformation efficiency. These research results provide a certain theoretical support for the implementation of China's innovation-driven development strategy, and related policies for promoting R & D innovation and export transformation in high-tech zones.