The grain production sector is a significant contributor to agricultural carbon emissions in China, and under the double pressure of the current ‘dual-carbon’ target and food security, clarifying the impacts of large-scale operation on the factor input structure and the efficiency of carbon emissions from grain production has become a key path to solving the problem of green and low-carbon transformation of China’s agriculture. This study explores the theoretical link between farm size and efficiency disparities, utilizing household survey data collected in 2023 from 1 150 households across Liaoning, Shandong, Sichuan, and Jiangxi provinces. Employing the Generalized Propensity Score Matching (GPSM) method under counterfactual assumptions, the paper estimates the average treatment effect of farm size on carbon emission efficiency in grain production. Additionally, regression adjustment and mediation effect models are employed to analyze underlying mechanisms, highlighting the mediating role of factor input structure. The findings indicate a “U-shaped” nonlinear relationship between farm size and carbon emission efficiency, underscoring the importance of optimizing factor input structure to leverage the positive impacts of farm size on carbon emission efficiency in grain production. Furtherly moderate expansion of farm size will support China’s pursuit of sustainable and green grain production. This research provides a scientific foundation for policymakers to guide rational scale management and resource optimization in the new development era, along with policy recommendations to promote green grain production through adjustments in factor input structure.