Environmental protection tax is an important tool for directing environmentally friendly growth in heavily polluting enterprises, but existing research has yet to provide consistent conclusions on whether and how environmental protection tax can promote green innovation in heavily polluting industries. The paper uses a double difference model based on data from Chinese listed companies in heavily polluting industries from 2012 to 2021 to empirically investigate whether environmental protection tax drives green innovation behavior of heavily polluting enterprises. The findings show that the environmental protection tax increases the degree of green innovation in heavily polluting enterprises, primarily through the anti-driving effect, in which an increase in environmental management expenses forces firms to increase their R&D investment, which improves the degree of green technical innovation. Furthermore, the environmental protection tax has a strong promotion effect on heavy polluters’ green innovation for state-owned enterprises and those in growing period or located in high marketization regions. However, this promotion effect is insignificant for non-state-owned enterprises and those in recession period, and environmental protection tax hinders green innovation of enterprises in mature period and those located in low marketization regions. Accordingly, it is suggested to improve preferential tax policies, increase investment in corporate green innovation and strengthen the supervision of environmental tax.