Abstract: The spatial development model with central cities and urban agglomerations as the main carriers is the key to promote coordinated regional development in our country. This paper starts from the perspective of city innovation, based on the method of difference in difference, and takes 210 cities of 19 urban agglomerations as the research object, empirically analyzes the effect of the construction of national central cities on the innovation ability of urban agglomerations, and uses intermediary methods to explore its mechanisms. The research results show that the construction of national central cities is conducive to the improvement of the innovation ability of urban agglomerations. And the results still remain robust by using different levels of data such as enterprises, industries, cities and different testing methods. The heterogeneity results show that the construction of national central cities has a higher effect on the innovation ability of urban agglomerations in eastern areas than in central and western regions; the larger the scale of national central cities expands, the more obvious the effect on improving the innovation ability of urban agglomerations is; the construction of national central cities has more effects on the innovation ability of technology-intensive industries than that of non-technology-intensive industries. The influence mechanisms indicate that the construction of national central cities affects the innovation ability of urban agglomerations by promoting the division of functions of urban agglomerations, knowledge spillover, market accessibility, and financial agglomeration. Further research shows that spatial distance is an important factor that affects the improvement of the innovation ability of urban agglomerations by the construction of national central cities. The effect of the construction of national central cities on the innovation ability of urban agglomerations has an inverted U-shaped relationship with spatial distance. At the same time, the effect of the construction of national central cities on the innovation ability of urban agglomerations depends on the development quality of the national central cities in the urban agglomerations, rather than the number of them. Therefore, we must adhere to the national center as the core to promote the rational division of labor in urban agglomerations, actively enhance the comprehensive strength of national central cities, balance the radiation effect and siphon effect of national central cities, and rationally plan the spatial layout of national central cities.