Based on the data of China’s heavily polluting listed enterprises from 2008 to 2019 and manually compiled data on the evolution of the river chief system, we use the double difference method to identify the policy impact of the river chief system on the green transformation. The empirical results show that, under the influence of environmental regulatory pressure caused by river chief system, heavy polluting enterprises are more inclined to adopt external acquisition strategy of green M&A rather than internal R&D strategy of green technology innovation to achieve green transformation. Further research shows that this phenomenon is more obvious when heavy polluting enterprises face greater media pressure or environmental uncertainty is low. The mechanism test shows that local governments may promote enterprises to make green transformation by tightening environmental regulations. Local governments should set clear targets for environmental control and urge heavily polluting enterprises to save energy and reduce emissions through institutional support and pressure, so as to alleviate pollution from the source.