Green innovation is vital for manufacturing enterprises to achieve a balance between economic, environmental and social benefits. This paper empirically investigates the mechanisms of government subsidies, R&D investment and public participatory environmental regulation on green innovation in manufacturing enterprises, selecting a sample of 1308 manufacturing firms listed on Chinese A-shares from 2010–2019. The results show that government subsidies can significantly promote green innovation in manufacturing enterprises, with private enterprises being more pronounced. R&D investment plays a mediating role in green innovation in manufacturing enterprises, while public participatory environmental regulation has a negative impact. The moderating effect of public participatory environmental regulation on government subsidies is different on different green patents, with a more negative effect on green invention patents than on green utility model patents. Public participatory environmental regulation has a negative moderating effect on the green innovation of state-owned manufacturing enterprises while having no significant effect on private manufacturing enterprises.