Ecological footprint is a key index to quantify the sustainability of regional natural capital utilization. Based on a three-dimensional ecological footprint (EF3D) model, this study evaluated the sustainable development of the urban agglomeration in the middle reaches of the Yangtze River Basin (UAMRYR), and introduced the disequilibrium index and environmental Kuznets curve to analyze the coordination between the ecological footprint index and socioeconomic development. The results show that: (1) Per capita biological capacity of the UAMRYR was decreasing while its per capita EF3D presented an increasing trend with an average annual growth rate of 6.81% , which led to serious ecological deficit. The inflection points of per capita EF3D of the Changsha-Zhuzhou-Xiangtan City Group (CZTCG) and Poyang Lake City Group (PYLCG) appeared in 2007 and 2009, respectively. The capital stock of regional grassland and cultivated land showed an increasing trend, while the capital flow of forestland and water areas could meet the demand of resource consumption. A serious loss of capital stock can be found in the UAMRYR, but the situation was better than that of the Chengdu-Chongqing and Yangtze River Delta City Groups. The sustainable utilization space of natural capitals in the PYLCG was better than that in the Wuhan urban agglomeration (WUG) and CZTCG. (2) There was a regional complementarity between footprint size (EFsize) and footprint depth (EFdepth), and areas with rich resources generally had lower EFsize and larger EFdepth. Cluster analysis showed that Jingmen, Xianning, and Xiangyang had a better pattern of natural capital utilization owing to their large EFsize and small EFdepth, while Wuhan, Ezhou, and Huanggang had a poor ecological sustainability owing to their small EFsize and large EFdepth. (3) The matching degrees of EF3D with water resources and population were poor. In comparison, a high matching degree was observed between EF3D and GDP. When the urbanization rate of the urban agglomeration reached a certain threshold, its relationship with per capita EF3D and EFdepth may change. The correlation between per capita EF3D and urbanization rate of the WUG, CZTCG, and PYLCG showed an inverted U shape. In addition, EFdepth of the PYLCG increased with the increase of urbanization rate, and the correlation between EFdepth and urbanization rate of the WUG and CZTCG accorded with the Kuznets curve. Findings can provide theoretical support for the sustainable use of natural capital and green development in the UAMRYR.