Based on the panel data sets of 273 prefecture-level cities from 2003 to 2018, China’s innovative city construction policy is treated as a quasi-natural experiment, the effect, mechanism and regional heterogeneity of innovative city construction on green technological innovation are evaluated by using difference-in-differences model. The results indicate that: the construction of innovative city has a significant positive effect on green technological innovation, and this effect exhibits lagging. The construction of innovative city can promote green technological innovation through government strategic guidance, innovative talents support and industrial structure optimization, but the mechanism of urban spatial expansion is not significant. The construction of innovative city has more significant positive effects on green technological innovation for the eastern cities, higher administrative level cities and cities in the two control zones.