The establishment of National Agricultural Green Development Pilot Zones (NAGDPZ) was regarded as a major policy initiative aimed at facilitating the green transformation of agriculture and was expected to significantly influence agricultural carbon emissions. However, limited research had been conducted in this area. Based on panel data from 284 cities spanning the period from 2013 to 2023, a quasi-natural experiment was constructed using the implementation of the NAGDPZ. The difference-in-differences (DID) method was employed to systematically evaluate the effect of the NAGDPZ policy on agricultural carbon emissions.The following findings were obtained:(1) The NAGDPZ policy was found to significantly reduce agricultural carbon emissions. A statistically significant negative effect at the 10% level was observed, with an estimated coefficient of -0.008. The robustness of this result was confirmed through parallel trend tests, placebo tests, propensity score matching DID (PSM-DID), exclusion of potential confounding policies, and controls for endogeneity.(2) Mechanism analysis revealed that the emission reduction effect was primarily driven by improvements in agricultural production efficiency, the development of digital inclusive finance, and the promotion of rural innovation and entrepreneurship. Specifically, the NAGDPZ policy had a significantly positive impact on agricultural total factor productivity, the digital inclusive finance index, and the rural innovation and entrepreneurship index, with coefficients of 0.019, 0.008, and 0.018, respectively.(3) Heterogeneity analysis indicated that the carbon reduction effect varied across regions. Significant negative impacts were observed in southern China, non-major grain-producing areas, and regions with higher levels of agricultural financial support, with coefficients of -0.008, -0.016, and -0.015, respectively. In light of these findings, it is recommended that the establishment of NAGDPZ be expanded to further enhance the policy's effectiveness in reducing agricultural carbon emissions.