<p>Whether the removal of regional administrative barriers can effectively coordinate intergovernmental relations and promote green and low-carbon development in border areas has become an important issue. This paper uses data from 285 prefecture-level cities in China from 2006 to 2020 to scientifically identify administrative boundary areas at the township level. It employs a multi-period difference-in-differences approach to examine the impact of the county-to-district policy on carbon emissions in these boundary areas. Our study finds that abolishing county-level administrations and establishing districts significantly reduces carbon emissions in administrative border areas. This effect is achieved by reducing segmentation in both factor and commodity markets. Further analysis reveals that the “proactive adaptation” type of policy has a significant carbon emission reduction effect in administrative border areas. Additionally, the policy is more effective in areas with weaker local government intervention, in eastern regions, and at urban borders. From the perspective of regional integration, this paper explores new pathways to address carbon emission gaps at administrative boundaries, providing theoretical support for strengthening the county-to-district transition and offering new ideas for the governance of carbon emissions in administrative boundary regions.</p>