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AbstractThe city is both a carrier and a subject of innovation. Based on the triple helix theory of industry–university research and the theory of spatial correlation, this study constructs a collaborative innovation framework both within the cities and between cities, and uses a network data envelopment analysis (DEA) model and spatial econometric model to measure and analyze the collaborative innovation efficiency in 75 innovative cities in China. The results show that collaborative innovation efficiency within cities is on the rise, and the efficiency of "research to production" is significantly higher than that of "learning to research." Industrial structure and foreign factors have inhibited the efficiency improvements, and infrastructure and living standards have different promoting effects on different stages of efficiency. Between cities, capital flows have obvious spillover effects, which promote the efficiency of innovation networks, while the long‐term characteristics of institutional learning have a near‐term negative impact.