Green government debt serves a dual role in supporting ecological and environmental protection initiatives while also alleviating local financial burdens, making it a vital green fiscal tool. This paper assesses the impact of green government debt on carbon emissions, focusing on China’s green special bond program from 2015 to 2021. The findings indicate that green government debt significantly reduces regional carbon emissions, particularly in key cities, cities southeast of the Hu Huanyong line, and resource-oriented cities. Further analysis reveals that green government debt effectively enhances energy consumption efficiency and stimulates social green investment. However, the issue of green government debt absorbing excessive financial resources persists, preventing the formation of a synergistic effect with green corporate debt. Based on these findings, this paper recommends issuing green government debt tailored to local conditions, clearly defining its scope, and exploring synergistic development models of green finance to achieve more efficient air pollution control.