<p>Can digitized supply chains be effective in mitigating the serious pollution problems in border areas caused by regional fragmentation and lack of regulatory cooperation? We attempt to deliver a response to this issue. This paper employs a difference-in-differences model, utilizing data from border cities between 2010 and 2022, to demonstrate that the “Supply Chain Innovation and Application Pilot” policy significantly enhances carbon emission efficiency in border regions, primarily by dismantling regional segregation and strengthening environmental regulatory capacity. Further analysis shows that boundary attributes reinforce to some extent the facilitating effect of supply chain digitization on carbon emission efficiency. In addition, the promotion effect of supply chain digitization on carbon emission efficiency is more prominent in border areas with lower levels of regional synergy and non-environmentally focused cities. This study provides a useful reference for improving the governance efficiency of administrative border areas in China.</p>