Abstract: Enhancing carbon total factor productivity (TFP) is the fundamental approach to achieving carbon peak and carbon neutrality in the agricultural sector. This study incorporates carbon emissions into the TFP analysis framework, using provincial data from China between 2000 and 2020 as a sample to estimate agricultural carbon emissions, including farmland use, rice cultivation, and livestock and poultry farming. The EBM-GML model and the comprehensive index method are employed to measure agricultural carbon TFP and environmental regulation index, respectively. Panel regression analysis is used to empirically test the impact of environmental regulation on agricultural carbon TFP and its mechanism. The results indicate that agricultural carbon TFP increased by 23.6% during the study period, achieving a significant growth. Environmental regulation significantly promotes the enhancement of agricultural carbon TFP, with both command-and-control and economic environmental regulations playing a significant positive role. When comprehensive environmental regulations, command-and-control environmental regulations, and economic-based environmental regulations each increase by 1 unit, agricultural carbon TFP will increase by 0.768, 0.823, and 1.034 units, respectively. We construct mediating effect model with technological innovation, industrial structure, and industrial agglomeration as mediating variables, and combine panel regression estimation with the bootstrap method to test the mechanism of environmental regulation affect agricultural carbon TFP. The mechanism test results reveal that command-and-control environmental regulations and economic environmental regulations both promote the improvement of agricultural carbon TFP by inspiring the positive role of technological innovation and suppressing the negative effects of industrial agglomeration in agriculture. Only economic environmental regulation positively affects agricultural carbon TFP by influencing the agricultural industrial structure, while the effect of command-and-control environmental regulation through this path is not significant. The study suggests that optimizing the agricultural environmental regulation system, promoting agricultural technological innovation, adjusting the agricultural industrial structure, and optimizing the agglomeration of agricultural industries will contribute to achieving the dual carbon goals in the agricultural sector.