The urban agglomeration in the middle reaches of the Yangtze River is the key area for the Central Region Rise Strategy in China. This area has long been confronted with the dilemma of development and protection. Research on the driving mechanism of ecological footprint from the perspective of spatial interaction of transportation network is of great significance for coordinating the high-quality socio-economic development and the high-level ecological civilization construction to achieve sustainable development. This paper internalizes the transportation network as a "channel" for the spatial interaction of ecological footprints between county units to explore the path of ecologically coordinated development. First, we used a ecological footprint model to assess the sustainable development level. The indicator of ecological footprint is an extensive and comprehensive measure of sustainable development. Second, complex network model was employed to characterize the scale and connectivity of the transportation network. Third, we established a transportation spatial interaction relationship based on the gravity model, and embed the "transportation" spatial weight matrix into the spatial econometric model. Integrated with the STIRPAT model, the model is established to explore the spatial effect of the transportation network on ecological footprint and the driving factors of ecological footprint. The results show that:(1) from 2010 to 2017, the average value of the ecological footprint for counties in the middle reaches of the Yangtze River has decreased from 1.73 to 1.66. (2) The scales of the road transportation network and the railway transportation network have both expanded, whereas the connectivity has decreased. (3) The spatial dependence of the ecological footprint was confirmed, and the ecological footprint shows a positive spatial spillover influence through the transportation network. This spatial influence had slighty enhanced from 2010 to 2017. The urbanization and per capita GDP have significantly positively influenced the ecological footprint, and the proportion of the tertiary sector to the total GDP negatively influenced ecological footprint. The research implies that the overall level of sustainable development of the middle reaches of the Yangtze River urban agglomeration has improved; the inter-regional sustainable development is strengthened by the spatial influence of the transportation network. In addition, socio-economic development has exacerbated unsustainability, while industrial transformation and upgrading showed a positive influence. In the future, while strengthening regional ecological integration based on transportation networks, a new pattern of sustainable development with regional linkages through the interaction of industries, exchange of resources, and sharing of technologies should be established.