PurposeThis study aims to analyze the relevance of the city spatial structure for smart city innovation from the perspective of agglomeration externalities, and discusses whether there is heterogeneity in innovation across different geographical areas and population scales of cities.Design/methodology/approachThe authors construct the centralization and concentration indexes to conceptualize the city spatial structure of 286 cities (prefecture-level) in China based on the LandScan Global Population Dataset from 2001 to 2016. A fixed-effects panel data model is employed to analyze the relationship between the spatial structure and the innovation ability of smart cities; the results were validated through robustness tests and heterogeneity analyses.FindingsThe study found that the more concentrated and more evenly the distribution of urban population, namely the more city spatial structure tends to be weak-monocentricity, the higher the level of innovation in smart cities. The relevance of the weak-monocentricity structure and smart city innovation varies significantly depending on their geographical location and the size of the city. This result is more applicable to cities in the eastern and central regions, as well as to cities with smaller populations.Originality/valueThe adjustment and optimization of the city spatial structure is important for enhancing smart city construction. Unlike previous studies, which mostly use a single dimension of “the proportion of population in sub-centres to the population of all central areas” to measure city spatial structure, the authors employed the spatial centralization and spatial concentration. It is hoped that this study can guide smart city construction from the perspective of the development model of city spatial structure.