Under the background of “dual carbon”, scholars are paying more and more attention to the inhibition effect of digital economy on agricultural carbon emissions. The results show that the development of digital economy has a significant inhibitory effect on agricultural carbon emission intensity. The interaction term between the constructed digital economy development index and the agricultural industry agglomeration level is negative, which proves that improving the agricultural industry agglomeration level is conducive to strengthening the inhibition effect of digital economy development on agricultural carbon emission intensity. According to the heterogeneity analysis based on whether the locational entropy representing agricultural industrial agglomeration is greater than 1, the results show that the digital economy has a more significant inhibitory effect on agricultural carbon emission intensity in regions with locational entropy greater than 1. Clarifying the impact mechanism of digital economy on agricultural carbon emission intensity can provide a path reference for the low-carbon sustainable development of China’s agriculture, and is of great significance for China’s agricultural modernization transformation.