Human social development has made ecological carrying capacity more fragile and sensitive, exacerbating the “butterfly effect” of expanding ecological footprints. However, the development of the digital economy has improved ecological efficiency, providing new opportunities to balance human social development and environmental protection. Nevertheless, existing literature lacks in-depth research on measuring ecological efficiency from the perspective of the balance between economic output and ecological footprint. In particular, it lacks thorough analysis of how the development of the digital economy affects ecological efficiency by embedding production efficiency and upgrading industrial structure at a deeper level of inherent logic. This paper believes that the rapid development of the digital economy plays an important role in achieving harmonious coexistence between humans and nature and enhancing ecological efficiency. Based on the provincial panel data from 2011 to 2019 in China, using the ecological footprint model and entropy-weighted TOPSIS method to respectively calculate the changes in the ecological footprint and the level of digital economic development in each province of China, and using per capita economic output and ecological footprint to measure ecological efficiency, this paper empirically tests the impact of the digital economy on ecological efficiency. The research found that the development of China’s digital economy has significantly improved the ecological efficiency of various regions. Mechanism tests show that the promotion effect of China’s digital economy development on ecological efficiency can be achieved through the mediation of production efficiency and industrial structure upgrades; threshold tests show that the higher the level of development of China’s digital economy, the stronger the enhancing effect on ecological efficiency, but under different production efficiency and industrial structure conditions, the impact of the digital economy on ecological efficiency is either a single threshold effect or no threshold effect; heterogeneity analysis shows that the impact of China’s digital economic development on ecological efficiency is heterogeneous. From the perspective of regional resource dependency, the promotion effect of the digital economy on ecological efficiency is stronger in non-resource-based areas than in resource-based areas. From the analysis of the policy nodes of the “Digital China” initiative, the post-node effect is stronger. Compared with existing literature, this paper mainly expands and deepens as follows: first, this paper measures ecological efficiency from the perspective of the ecological footprint and economic output, reflecting the impact of economic development on the ecological environment with an ecological footprint, revealing the changing laws and inherent logical relationships between the ecological footprint and ecological efficiency. Second, this paper puts the digital economy, ecological footprint, and ecological efficiency in the same analytical framework and conducts an in-depth analysis of the impact of the digital economy on ecological efficiency based on the changes in ecological footprints in various regions of China. Thirdly, unlike existing literature that focuses solely on the role of industrial structure upgrades or green ecological efficiency on ecological efficiency, this paper comprehensively analyzes the mechanism of the digital economy on ecological efficiency from the aspects of production efficiency and industrial structure upgrades, and empirically tests the mechanism and non-linear characteristics of the digital economy in enhancing ecological efficiency. This study deepens the connotation and measurement methods of ecological efficiency, to a certain extent, reveals the inherent logical relationship between the digital economy and ecological efficiency, and helps governments at all levels formulate policy measures for the development of the digital economy from the aspects of improving resource utilization efficiency, promoting green technology innovation and research and development, optimizing industrial structure, and strengthening the construction of digital infrastructure.