<p>With the goal of carbon peak and carbon neutral, increasing carbon emission efficiency has become a critical point in Chinese economic development. Based on Chinese provincial panel data and the DEA model, this paper explores regional protection’s impacts and transmission mechanism on carbon emission efficiency. The heterogeneity of impacts, the interaction of adjacent areas, and the role of carbon emission trading in the impact of regional protection on carbon emission efficiency are further explored. The results show that regional protection can reduce carbon emission efficiency by restraining technical efficiency, allocative efficiency, scale efficiency, and total factor productivity of gross product per unit of carbon emission. In addition, regional protection has a stronger impact on provincial regions with lower carbon emission efficiency, and regional protection in neighboring regions also has a significant negative impact on carbon emission efficiency of the local region. Finally, implementing carbon emission trading significantly reduces the negative impact of regional protection on carbon emission efficiency.</p>