Climate change poses a significant threat to the sustainable development of all countries. The transition to low-carbon energy sources is a crucial strategy for reducing carbon emissions and mitigating climate change. We investigate the mediating role of clean energy consumption (EC) and fossil energy supply (ES) on the promoting of carbon emission intensity per unit of GDP (CO2/GDP) reduction by green bonds (GBs). We develop a mediating model to analyze how GB influences CO2/GDP reduction through EC and ES, utilizing panel data from 13 prefecture-level cities in Jiangsu province spanning the years 2007 to 2021. Additionally, we assess the model’s reliability through endogeneity and robustness tests. We find that GBs contribute to reducing CO2/GDP by facilitating the structural transition of energy supply and consumption. Furthermore, the development of GBs enhance the consumption of clean energy and plays a direct role in advancing the transition in structure of both energy supply and energy consumption. Notably, we observe heterogeneity in the effectiveness of GBs on CO2/GDP reduction across different regions. Therefore, it is imperative for the government to actively promote the development of GBs to achieve sustainable economic growth. Furthermore, both financial and energy policies should be tailored to align with the specific energy structures of various regions.