Abstract: Enhancing carbon total factor productivity (TFP) is a fundamental approach to achieving carbon peaks and carbon neutrality in the agricultural sector. This study incorporated carbon emissions into the TFP analysis framework using provincial data from China between 2000 and 2020 to estimate agricultural carbon emissions, including farmland use, rice cultivation, and livestock and poultry farming. The EBM-GML model and comprehensive index method were employed to measure the agricultural carbon TFP and the environmental regulation index, respectively. A panel regression analysis was used to empirically test the impact of environmental regulations on agricultural carbon TFP and its mechanism. The results indicated that agricultural carbon TFP increased by 23.6% during the study period, achieving significant growth. Environmental regulations significantly promoted the enhancement of agricultural carbon TFP, with both command-and-control and economic environmental regulations playing significant positive roles. When comprehensive environmental regulations, command-and-control environmental regulations, and economy-based environmental regulations each increased by one unit, agricultural carbon TFP increased by 0.768, 0.823, and 1.034 units, respectively. We constructed a mediating effect model with technological innovation, industrial structure, and industrial agglomeration as mediating variables, and combined panel regression estimation with the bootstrap method to test the mechanism of environmental regulation affecting agricultural carbon TFP. The mechanism test results reveal that command-and-control and economic environmental regulations 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, whereas the effect of command-and-control environmental regulation through this path is not significant. This 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.