Heavy-polluting enterprises are a vital component of China's industrial system, and their low-carbon transition serves as a critical pathway for achieving carbon peaking and carbon neutrality goals. The pilot zones for green finance reform and innovation (PZGFRI) in five provinces and eight cities from 2017 were employed as an exogenous shock, and the data from A-share listed enterprises during the period from 2012 to 2021 were utilized. A difference-in-differences-in-differences model (DDD) was constructed to systematically evaluate the policy's impact on the carbon emissions of heavy-polluting enterprises and its transmission mechanisms. The results reveal that PZGFRI significantly reduces carbon emission among these enterprises. This effect is found to initially strengthen and subsequently weaken post-implementation. Mechanism tests indicate that the policy functions through three channels: fund support, technological innovation, and environmental awareness. At the regional level, the expansion of green credit scale and the further development of green insurance are promoted in the pilot areas. At the enterprise level, the policy is shown to guide improvements in both the quantity and quality of green innovation. It is also found to enhance the environmental protection awareness of senior executives. Heterogeneity analysis indicates more pronounced policy effects in state-owned enterprises, highly financialized firms, and enterprises with superior capital allocation efficiency. This further demonstrates that PZGFRI effectively supports carbon reduction through corporate utilization of financial instruments and rational capital allocation. It provides micro-level evidence for optimizing green finance policy portfolios and establishing differentiated regional promotion mechanisms.