Abstract: Improving agricultural production efficiency under carbon emission constraints is an important driving force for promoting the high-quality development of modern agriculture in China. The digital economy promotes the green development of agriculture and improves the agricultural production efficiency by optimizing the allocation of agricultural resources. This study used panel data from 30 provinces (autonomous regions and municipalities, not including Hong Kong, Macao, Taiwan and Xizang of China) in China from 2011 to 2021 to measure the development level of regional digital economy and agricultural production efficiency under carbon emission constraints. From the perspective of industrial structure, this paper examined how the digital economy affected agricultural production efficiency under the constraint of carbon emissions by influencing rural three-industry integration with the levels of rural human capital and agricultural technological innovation as regulating variables. The empirical results showed that in general, the development of the digital economy has improved agricultural production efficiency under the constraint of carbon emissions in China, and the conclusion remained significant after a series of robustness tests and endogeneity discussions. The mediating effect analysis showed that the digital economy improved agricultural production efficiency under carbon emission constraints by promoting the integration of rural three-industry and that the digital economy has a significant role in promoting the extension of the agricultural industry chain and multi functional expansion of agriculture. Progress in agricultural technological innovation and the improvement of rural human capital have strengthened the role of the digital economy in promoting carbon-constrained agricultural production efficiency. In the non-pilot zone of rural industry integration, eastern regions and major grain-producing areas, the development of the digital economy more significantly promoted the improvement of agricultural production efficiency under the constraint of carbon emissions. From the perspective of the digital economy, this research provides policy insights to improve agricultural production efficiency under China’s carbon emission constraints and helps modern high-quality agricultural development.