As an important node and industry of regional innovation, national independent innovation demonstration zone has shown a trend of setting up units based on urban high-tech zones in recent years. In this paper, DEA method and Malmquist index method are used to conduct static and dynamic research on the innovation efficiency of high-tech zones in 14 provinces and cities of China"s six major urban agglomerations from the perspective of regions and urban agglomerations respectively, based on the panel data from 2013 to 2017.The results show that the innovation efficiency of high-tech zones in the six major urban clusters keeps increasing. From the regional perspective, the growth of innovation efficiency shows a trend of "high in the West and low in the East". From the perspective of urban agglomeration, the internal innovation efficiency of urban agglomeration is unbalanced. Through the decomposition of innovation total factor productivity in regional and urban agglomeration, it is found that the change of technical efficiency is the main factor affecting innovation efficiency, and the improvement of pure technical efficiency and scale efficiency has become a new growth point of innovation efficiency. Finally, according to the conclusion, corresponding policy Suggestions are put forward to provide reference for further improving the innovation capacity construction of high-tech zones.