Green transformation is essential for the high-quality development of heavy polluting enterprises and the realization of China’s modernization. Green mergers and acquisitions (M&A) are an important strategy for achieving this goal. This study employs the central environmental protection supervision policy as a quasi-natural experiment and constructs a multi-time point difference-in-differences model using data from A-share listed heavy polluting enterprises from 2010 to 2023. The empirical results show that the central environmental protection supervision system has a positive impact on the Green M&A behavior of heavy polluting enterprises. From a mechanistic perspective, the central environmental supervision system primarily promotes Green M&A through two pathways: enhancing internal environmental performance and increasing external legitimacy requirements. Further analysis reveals that the promotion effect is more pronounced in central and western regions and in enterprises more prone to “government-enterprise collusion”. This study elucidates the relationship between the central environmental protection supervision system and the Green M&A of heavy polluting enterprises, contributing to a deeper understanding of corporate green transformation and the micro-impact of environmental supervision systems, and leverage Green M&A to achieve a ‘win-win’ in environmental and economic benefits.