The construction of national high-tech zones is an important measure to improve China's independent innovation ability. And it is of great significance to the strategy of innovative national construction. The free trade zone is an important platform for China to establish a new system for high-level open economy. The outline of the National 14th Five-year Plan clearly stresses the significance of "strengthening the innovation function of high-tech industrial development zones" and "giving free trade zones greater autonomy in reform and innovation". It has become an important measure for China to accelerate the high-quality development of national high-tech zones and free trade zones to promote the strategy of innovation-driven development as well as the reform and opening-up policy. In recent years, the geographical overlap between the national high-tech zone and the free trade zones has become increasingly obvious. The construction emphasis and objectives of these two types of zones are also highly consistent. It has become a practical issue to promote the joint innovation of high-tech zones and free trade zones. More importantly, this is in line with the internal requirements of building a new development pattern. It is very challenging to objectively evaluate the innovation efficiency of high-tech zones and accurately identify the mechanism of the free trade zone policy. #br#Therefore, on the basis of literature and theoretical analysis, this paper aims to clarify the internal mechanism of the joint innovation between high-tech zones and free trade zones, and also makes an empirical study on the impact of the establishment of the free trade zones on innovation efficiency of high-tech zones. This will help give better play to the policy superposition effect of free trade zones and high-tech zones, and build the two types of zones into important nodes of the "dual circulation" development pattern. Specifically,based on the theoretical analysis, this study discusses the theoretical mechanism of the impact of the establishment of free trade zones on the agglomeration level of innovation resources and the innovation efficiency of high-tech zones. Then drawing on the panel data of 34 national high-tech zones and their cities from 2007 to 2020, it uses DEA-Malmquist model to measure the innovation efficiency index of high-tech zones, and also uses the time-varying DID method to evaluate the impacts of free trade zones on the agglomeration level of innovation resource and the innovation efficiency of national high-tech zones. #br#Through the theoretical analysis and empirical analysis, the main conclusions are drawn as follows. First, the mean values of innovation efficiency index, technical efficiency index and technical progress index of both the treatment group and the control group are greater than 1. Among them, the mean value of technical progress index is greater than the mean value of technical efficiency index. This shows that the innovation efficiency of the high-tech zones was improved from 2007 to 2020, and itmainly depended on the improvement of technical progress rather than technical efficiency. Second, the establishment of the free trade zones has a significant positive impact on the agglomeration level of innovative resources of high-tech zones, and it is manifested in three aspects: the agglomeration of high-tech enterprises, the growth of R&D expenditure and the growth of R&D personnel. Third, the establishment of the free trade zones does not significantly improve the innovation efficiency of the high-tech zones. In view of the decomposition of innovation efficiency, the reason is that although the establishment of the free trade zone has significantly improved the technical efficiency of the high-tech zones,it has not significantly improved the technical progress of the high-tech zones. These conclusions suggest that the free trade zones should draw upon the institutional advantages and promote the in-depth reform so that more high-quality innovation elements can be gathered. Then on the basis of the agglomeration of high-tech enterprises and the increase of R&D investment, the high-tech zones should further strengthen their innovation ability and improve the utilization efficiency of innovative resources and the conversion efficiency of technological achievements. Finally, the government should open up the institutional and market channels between the free trade zones and the high-tech zones, and integrate the construction of the free trade zones with the high-tech zones, so as to enhance the policy synergy of the two zones and form complementary advantages.#br#