<p>Despite the increasing literature on China’s progress toward agricultural decarbonization in the context of rural digitalization, its mechanism has not been thoroughly investigated. To fill the research gap, we conducted an empirical study with a panel data of 30 provinces in China and employed a series of mediation models to examine the association between rural digitalization and agricultural carbon efficiency while incorporating the evolution of agricultural productivity and production structure, with robustness ensured via alternative specifications, difference-in-differences method and instrumental variable (IV) approaches. Overall, the results demonstrate that rural digitalization has a significantly indirect influence on agricultural carbon efficiency, which is fully mediated by agricultural productivity and production structure. However, the impact of rural digitalization on agricultural carbon efficiency has remarkable regional heterogeneity. The mediation effect of agricultural productivity is more significant in the eastern/coastal and main grain-producing areas. In contrast, the mediation effect of agricultural production structure is more significant in the central/western and non-main grain-producing provinces. Furthermore, the results show that agricultural productivity and production structure has threshold effects on the association between rural digitalization and agricultural carbon intensity. These findings indicate that the government should promote rural digitalization to attain agricultural carbon neutrality without compromising food security. Additionally, China’s experience illustrates that the design and implementation of rural digitalization and agricultural decarbonization policies should be tailored to local nuances and coordinated with each other.</p>