<p>The drive of the rural digital economy in agricultural development and the enhancement of agricultural net carbon efficiency are integral to ensuring the quality development of agricultural ecology. To better understand the impact of the digital economy on agricultural ecological quality, this paper utilizes panel data from 30 provinces (municipalities, autonomous regions) in China from 2013 to 2020 and employs the instrumental variable method to analyze the impact of digital economy development on agricultural net carbon efficiency. The results reveal that the advancement of the rural digital economy significantly enhances the net carbon efficiency of agriculture, and this finding remains robust even after substituting explanatory variables and excluding samples from direct-administered municipalities. Heterogeneity analysis indicates that the aforementioned impact is more pronounced in major grain-producing areas, regions with high agricultural industrial concentration, and areas with low government intervention. Further analysis reveals that the rural digital economy can enhance agricultural net carbon efficiency through two primary mechanisms: improving human capital and promoting technological progress. The conclusions of this study have significant implications for improving the level of rural digital economy development and optimizing agricultural net carbon efficiency.</p>