Abstract: The pilot policy of national innovative cities has been gradually extended to the whole country. However, under the unique governance structure of China, whether this kind of experimental principal governance can be transformed into governance efficiency and its spatial spillover effect are rarely studied from an empirical point of view. Using the panel data of 270 cities at or above prefectural level, this study takes the pilot establishment of national innovative cities as a natural experiment, and uses the double difference method to investigate the policy effect. The main results are as follows: (1) the national innovative city pilot policy has a significant effect on the promotion of urban innovation, but the dynamic effect shows that it has a weakening trend year by year.(2) the results of heterogeneity test show that the effect of innovative urban pilot policy shows a differential order pattern in the eastern, central and western regions. (3) further research on spatial Dubin effect shows that the pilot policy of innovative cities has spatial spillover effect, which not only promotes the improvement of urban innovation in pilot areas, but also has a significant impact on the innovation of neighboring cities. The level of financial development and industrial structure can effectively promote the level of local innovation, and have spillover effects on neighboring areas, while human capital has crowding out effect on the promotion of innovation in neighboring areas. The robustness test supports the above conclusions. Based on the empirical results, this paper puts forward some policy suggestions, such as promoting the orderly diffusion of innovative cities, strengthening the spatial radiation effect of policies, designing the gradient development strategy of innovative urban policies, and promoting the coordinated development of regions.