ABSTRACT This study aims to explore the impact of innovation agglomeration on air pollution and industrial transformation within the context of China’s green development transition. We developed a general equilibrium model to theoretically explore these effects and employed an econometric analysis using panel data from 284 prefecture-level cities in China between 2005 and 2019 to empirically validate our findings. The main results are as follows: (1) Innovation agglomeration can significantly improve air quality, with a strong spatial spillover effect. (2) Innovation agglomeration can significantly promote transformation and upgrading of industrial structure, and it may also lead to the convergence of some industrial structures. Moreover, industrial structure transformation and upgrading partially mediates the relationship between innovation agglomeration and air pollution. (3) There is a nonlinear relationship between innovation agglomeration and air pollution. As industrial complementarity is developed, the effect of innovation agglomeration on air pollution enhances. These findings suggest that fostering innovation clusters and encouraging industrial diversification are key policy strategies for achieving sustainable urban development and improving environmental outcomes.