Abstract: Effectively alleviating the threat of resource and environmental constraints on grain production and improving grain eco-efficiency are inevitable choices to continuously build the “fortress” of China’s grain security. As a new economic form accompanying the changes in information technology, the digital economy can promote high-quality development of the grain industry both directly and indirectly. Based on the panel data of 13 major grain-producing areas from 2013 to 2021, this study constructed digital economy indicators from the two dimensions: digital industrialization and industrial digitalization. The development level of the digital economy and grain eco-efficiency was measured using the entropy weight method. The impact mechanism of the digital economy on grain eco-efficiency was analyzed in multiple dimensions using baseline regression, intermediary effect, and threshold effect models, which were of great significance for clarifying the correlation between them. The results indicated that the overall grain eco-efficiency of the 13 major grain-producing areas showed an increasing trend from 2013 to 2021, divided into three stages: rapid decline, rapid increase, and slow increase. Moreover, there were clear spatial differences in grain eco-efficiency, indicating that the growth rate of grain eco-efficiency in the northern region was higher than that in the southern region. The digital economy had a significant positive impact on grain eco-efficiency, and this conclusion remained valid after a series of robustness tests, such as adjusting sample intervals, eliminating outlier estimates, and lagging explanatory variables. Heterogeneity analysis revealed that digital industrialization had a more significant promoting effect on grain eco-efficiency than industrial digitalization, and that the digital economy had a more significant promoting effect on grain eco-efficiency in the northern regions and regions with low grain eco-efficiency. The intermediary effect analysis showed that the scale of agricultural land management and agricultural socialization services significantly promoted grain eco-efficiency. This indicates that the digital economy can indirectly improve grain eco-efficiency by expanding the scale of agricultural land management and improving agricultural socialization services. The threshold test results suggested that the promoting effect of digital economy on grain eco-efficiency was influenced by the intensity of fiscal support for agriculture and presented a nonlinear feature of increasing marginal effects; that is, the higher the intensity of fiscal support for agriculture, the more the digital economy could improve grain eco-efficiency. To continuously improve grain eco-efficiency, it is necessary to enhance the construction of a new rural digital infrastructure, increase the scale of agricultrual land management and agricultural socialization, optimize the structure of fiscal support for agriculture, highlight the development orientation of green policies, and adopt a differentiated collaborative promotion strategy for the digital economy and grain eco-efficiency.