Abstract: Improving agricultural production efficiency under carbon emission constraint is an important driving force to promote the high-quality development of modern agriculture in China. The development of digital economy promotes the green development of agriculture and improves the efficiency of agricultural production by optimizing the allocation of agricultural resources. Based on the characteristics of digital economy affecting agricultural production efficiency under carbon emission constraints, this study uses the panel data of 30 provinces and municipalities 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, taking rural three-industry integration as a mechanism variable, this paper studies the mechanism of digital economy affecting agricultural production efficiency under the constraint of carbon emission by influencing rural three-industry integration. Taking the level of rural human capital and scientific and technological progress as the regulating variables, the impact of digital economy on agricultural production efficiency under the constraint of carbon emission is analyzed. The empirical results show that: (1) In general, the development of digital economy has improved the agricultural production efficiency under the constraint of carbon emissions in China, and the conclusion is still significant after a series of robustness tests and endogeneity discussions. (2) Mediating effect analysis shows that, digital economy can improve agricultural production efficiency under carbon emission constraints by promoting the integration of rural three industries, and digital economy has a significant role in promoting the extension of agricultural industry chain and the expansion of agricultural multifunction. (3) The progress of agricultural science and technology innovation and the improvement of rural human capital have strengthened the role of digital economy in promoting carbon-constrained agricultural production efficiency. (4) The integration of rural three production areas in non-pilot areas, eastern regions and main grain producing areas, and the development of digital economy more significantly promoted the improvement of agricultural production efficiency under the constraint of carbon emissions. From the perspective of digital economy, this research provides policy enlightenment to improve agricultural production efficiency under China’s carbon emission constraints, and then help modern agricultural high-quality development.