Introduction: Digital transformation has become an important engine for economic high-quality development and environment high-level protection. However, green total factor productivity (GTFP), as an indicator that comprehensively reflects economic and environmental benefits, there is a lack of studies that analyze the effect of digital transformation on heavily polluting enterprises' GTFP from a micro perspective, and its impact mechanism is still unclear. Therefore, we aim to study the impact of digital transformation on heavily polluting enterprises' GTFP and its mechanism, and explore the heterogeneity of its impact. Methods: We use Chinese A-share listed enterprises in the heavily polluting industry data from 2007 to 2019, measure enterprise digital transformation indicator using text analysis, and measure enterprise GTFP indicator using the GML index based on SBM directional distance function, to investigate the impact of digital transformation on heavily polluting enterprises' GTFP. Results: Digital transformation can significantly enhance heavily polluting enterprises' GTFP, and this finding still holds after considering the endogenous problem and conducting robustness tests. Digital transformation can enhance heavily polluting enterprises' GTFP by promoting green innovation, improving management efficiency, and reducing external transaction costs. The improvement role of digital transformation on heavily polluting enterprises' GTFP is more obvious in the samples of non-state-owned enterprises, non-high-tech industries, and the eastern region. Compared with blockchain technology, artificial intelligence technology, cloud computing technology, big data technology, and digital technology application can significantly improve heavily polluting enterprises' GTFP. Discussion: Our paper breaks through the limitations of existing research, which not only theoretically enriches the literature related to digital transformation and GTFP, but also practically provides policy implications for continuously promoting heavily polluting enterprises' digital transformation and facilitating their high-quality development.