As the strategic frontier of cultivating new growth momentum and reshaping the regional competition pattern, the relationship between the low-altitude economy and urban innovation capacity needs to be tested empirically. Based on the panel data of Chinese cities from 2000 to 2023, this study empirically examines the impact and mechanism of low-altitude economic development on urban innovation capacity by using a fixed effect model. The research finds that a low-altitude economy significantly promotes urban innovation capacity. The mechanism test indicates that such an impact is mainly achieved through three paths: “biased knowledge network reconstruction”, “reconfiguration and optimization of production factors” and “forcing and friction of institutional adaptability”. Further heterogeneity analysis reveals the differential performance of this effect in various regions, and the conclusion remains valid after a series of robustness tests. This study not only enlightens a new theoretical perspective for understanding the complex interaction between emerging business formats and urban innovation system, but also provides empirical evidence and policy implications for local governments to accurately improve innovation through the development of a low-altitude economy.