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Regional reassessments of agricultural carbon emission efficiency are essential for improving the sustainability of food production systems under climate constraints. This study evaluates agricultural carbon emission efficiency (ACEE) across China’s major grain-producing zone (GPZ), major grain-consuming zone (GSZ), and grain production–consumption balanced zone (GBZ) during 2003–2022, excluding Hong Kong, Macao, Taiwan, and Tibet due to data limitations. A super-efficient EBM–GML model incorporating both desirable and undesirable outputs is employed to measure ACEE at the provincial level, with comparisons conducted within each functional zone and nationally unified efficiency values used as a benchmark. Spatial dependence is examined using Moran’s I, and a spatial Durbin model is applied to identify driving factors and spatial spillover effects. The results indicate that the average efficiency levels differ systematically across functional grain zones, following the order GBZ > GPZ > GSZ, while several provinces experience notable changes in their relative rankings. Carbon emissions increase in the earlier period and decline in later years, whereas efficiency exhibits an opposite temporal pattern, reflecting a gradual transition of grain production systems from extensive input-driven growth toward more sustainability-oriented practices. Substantial regional disparities in ACEE are also observed. Rational industrial organization and efficient allocation of production resources contribute to positive spillover effects on neighboring regions, whereas natural disasters and inefficient resource distribution tend to weaken such effects. These findings suggest that functional grain zones provide an effective framework for capturing intra-regional heterogeneity and should be adopted as the basic unit for efficiency assessment and the formulation of differentiated governance strategies.