Rapid urbanization in urban agglomerations has resulted in serious degradation of ecosystem functions and deterioration of ecosystem health, which hinders the current process of new-type urbanization and ecological civilization construction in China. Healthy ecosystem in urban agglomerations is closely related to the sustainability of urban agglomerations. The scientific assessment of the ecosystem health status has important practical significance for the formulation of macro-control policies for ecosystem health in the urban agglomerations, but the current studies about the ecosystem health evaluation in urban agglomerations were still insufficient. An increasing number of studies have been carried out on the theories, concepts, spatiotemporal differentiation characteristics, and influencing factors of ecosystem health, but few studies have included the results of ecosystem services assessment based on InVEST model into the theoretical framework of ecosystem health assessment. Ecosystem services assessment is an important part to reflect the health status of the ecosystem. Ecosystem services assessment based on InVEST model can well reflect the structure, function, and ecological process of ecosystem services, and realize the spatial and dynamic quantitative assessment of ecosystem services. How to integrate ecosystem services into the framework of ecosystem health assessment has become a hot topic of the current studies. Based on the ecosystem services evaluated by InVEST model, this study constructed the ecosystem health assessment framework system of "Vigor-Organization-Resilience-Ecosystem Services", and evaluated the ecosystem health level in the Middle Reaches of the Yangtze River Urban Agglomerations (MRYRUA) with multi-source data. The results showed that:(1) the ecosystem health index in Jianghan Plain, Dongting Lake Plain, Wuhan, Changsha, Nanchang, and other surrounding counties was mostly below 0.35, while the ecosystem health index of the surrounding mountainous counties was more than 0.65. In addition, the ecosystem health index of units along major traffic routes was lower than that of other regions. The overall ecosystem health status in the MRYRUA deteriorated during the study period, mainly in the core areas of these urban agglomerations. (2) The ecosystem health in the MRYRUA showed significantly spatial dependence during the study period, the high-valued areas of ecosystem health were mainly distributed in the surrounding mountainous areas and the central Luoxiao Mountains, while the low-valued areas of ecosystem health were mainly distributed in the plain areas, the surrounding areas of key cities, and the areas along the main traffic routes. The results of the study can provide scientific support for ecosystem health assessment in other regions and ecosystem health protection policy-making in the MRYRUA.