Abstract: Agriculture are second largest source for greenhouse gases emissions (carbon emissions), which is second only to those from industry. Crop production sytem is the foundation of agriculture. Therefore, carbon emission reduction in crop production system is critical to realizing the goal of “double carbon”. Under the “carbon peak and carbon neutral” emission pattern, the digital economy has become a novel engine to promote the green, low-carbon, and high-quality development of crop production system. In this study, based on theoretical discussion and panel data of 31 provinces (autonomous regions and municipalities, excluding Hong Kong, Macao and Taiwan) in China from 2011 to 2021, the carbon emission efficiency of crop production system and the comprehensive development level of the digital economy in each province were measured using the Super-efficient SBM-Undesirable model, the Malmquist-Luenberger productivity index decomposition method, and the entropy value method. Based on the development level of each province, this study used the fixed effects model, instrumental variable, mediation effect, and threshold effects models to empirically examine the intrinsic relationship between digital economic development and carbon emission efficiency in crop production system. The study reveals that: 1) digital economic development has a significant positive impact on the carbon emission efficiency of crop production system with heterogeneity in different agricultural production functional regions as well as geographical zone; 2) digital economic development suppresses the carbon emission from crop production system by promoting technological innovation and large-scale operations; 3) the “technological innovation effect” contributes significantly more to the mediating effect than does the “large-scale operation effect;” 4) the impact of digital economic development on carbon emission efficiency in crop production system is also influenced by the economic development level. When the level of economic development is lower than the threshold, the impact of digital economic development on carbon emission efficiency in crop production system is not significant. When the level of economic development exceeds the threshold, digital economic development has the potential to significantly improve carbon emission efficiency in crop production system. Given this, this study puts forward the following countermeasures. 1) Build a complete and perfect digital infrastructure to promote the high-quality development of the digital economy and deepen the integration and application of digital science and technology in crop production system. 2) Focus on supporting the scale of crop production system and information technology. 3) Promote the synergistic development of both the digital and regional economy. 4) Set up inter-regional cooperation mechanisms to strengthen connectivity and information sharing among regions, and a differentiated, dynamic, and uneven development strategy should be implemented according to local conditions.