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Although constructing innovative cities stimulates innovation, it may further widen regional innovation differences. Based on panel data from 275 cities in China from 2003 to 2020, the difference-in-differences method was used to examine the impact of the innovative city pilot policy on urban innovation convergence. The study finds that the pilot policy not only improves the innovation level of cities (basic effect) but also promotes innovation convergence among pilot cities (convergence effect). However, in the short-term, the policy slows the innovation convergence of the entire region. The results reveal the innovative city policy’s multiple effects and dual character and capture the spatial spillover and regional heterogeneity of policy impact, highlighting the risk of further marginalizing some cities. This study supplements the evidence that government intervention affects regional innovation patterns based on the place-based innovation policy in China, providing theoretical support for expanding the follow-up pilot scope and the coordinated development of regional innovation.