A fundamental shift in the regional development pattern is crucial to achieving a comprehensive green transformation in China. Currently, innovation-driven green development is a significant strategic option for regional development. As the main body of innovation and the basic unit of regional composition, enterprises have a profound impact on the development of regional economy, society, ecology, and other aspects. However, considering China’s vast territory and significant regional differences in natural environment and industrial structure, it’s necessary to further explore the specific impact paths of regional green development driven by enterprise innovation. Therefore, taking industrial enterprises as an example, based on the panel data of 30 provinces in China from 2016 to 2020, this study verifies the impact of industrial enterprise innovation on the regional green development level by constructing a parallel multiple mediating effect model and dividing the economy into eastern, central, and western regions to discuss the specific impact paths. The results show that industrial enterprise innovation has a significant positive effect on regional green development level, via different influencing paths in each region: (1) The eastern region improves the regional green development level by narrowing the urban-rural income gap; (2) The central region improves the regional green development level by reducing resource dependence; and (3) The western region raises the regional green development level by improving the rationalization of industrial structure.