Reducing carbon emissions in agricultural production helps achieve green agricultural development in the Yellow River Basin, China. Exploring the influence of high-quality development (HQD) on agricultural carbon emissions (ACE) is of great significance for implementing low-carbon agriculture. Using the panel data of 76 prefecture-level cities from 2005 to 2021, this paper analyzes the influence and mechanism of HQD on ACE using the static and dynamic spatial Durbin, mediating effect, and panel threshold models. Results show that carbon emissions from chemical fertilizers are the highest, above 13 million tons. ACE in the eastern part is higher than in the western part. Empirical analysis manifests that HQD correlates with ACE negatively, accompanied by a substantial negative spatial spillover effect. The long-term effects of HQD, with estimated direct and indirect coefficients of -0.771 and -1.461, are obviously greater than the short-term effects, with estimated coefficients of -0.263 and -0.469. In addition, industrial structure upgrading plays a mediating role in the relationship between HQD and ACE. Furthermore, there is a non-linear relationship between HQD and ACE. When the degree of urbanization and economic development exceeds the threshold value, the effect of HQD on ACE shifts from promotion to inhibition. These results have guiding significance for low-carbon and sustainable agricultural practices.