The urban agglomeration in the middle reaches of the Yangtze River is within a typical ecologically sensitive area as well as a key development area in China. Scientific assessment of its ecological carrying capacity has important scientific value and practical significance. On the basis of both the components and structural characteristics of urban ecosystems, in this study, we used state-space techniques to construct a comprehensive evaluation index system for the urban ecosystem carrying capacity from three dimensions:socio-economic coordination, resource and environmental supply, and ecological elasticity. Spatial analysis, multiple regression, and geographically weighted regression were used to analyze the temporal-spatial patterns and other factors influencing the urban ecosystem carrying capacity in an urban agglomeration in the middle reaches of the Yangtze River from 2006 to 2015. The results indicated that:(1) the urban ecosystem carrying capacity of study area presents a W-shaped fluctuating increasing trend. The dimension of socio-economic coordination follows a fluctuating decreasing tendency, while the dimensions of resource and environment supply and ecological elasticity are increasing with fluctuations. (2) With regard to the perspective of spatial patterns, the urban ecosystem carrying capacity of study area is characterized by an obvious space correlation and heterogeneity. Two hot spots formed in the Poyang Lake urban agglomeration and the area around the Dongting Lake, and two cold zones formed in the core area of the Wuhan urban agglomeration and the urban agglomeration around Changsha-Zhuzhou-Xiangtan. (3) The factors of social development level, income level of urban inhabitants, population density, economic development efficiency, resource supply level, and environmental pollution control level exert significant effects on the spatial differentiation pattern of the urban ecosystem carrying capacity in urban agglomeration in the middle reaches of the Yangtze River. Moreover, the intensity shows a spatial heterogeneity characteristic.