The design of ecological compensation mechanisms in urban agglomerations of watersheds that span a large spatial range are similar. They are based on factors including similar geographical locations, nature resource endowments, and social economic structures. However, the design of ecological compensation mechanisms among different urban agglomerations is quite different based on the factors above. Moreover, the study of individual urban ecosystems and their collaborative management cannot fundamentally solve regional (including river basins in an urban agglomeration and urban agglomerations in a river basin), ecological, or environmental problems. From the perspective of urban agglomeration, the study of regional coordinated development can improve the degree of cooperation among cities and coordination of policy formulation. It can also provide new ideas for the study of river basin ecological/environmental governance and the balance of supply and demand for ecosystem services. Taking the Yangtze River basin as an example, we studied the ecological compensation mechanism of typical urban agglomerations, compared the differences and similarities in the design of ecological compensation mechanisms between different urban agglomerations, and formed the design innovation for the ecological compensation mechanism of the Yangtze River basin. Finally, we provide policy suggestions for innovating the long-term mechanism of ecological compensation based on urban agglomeration and coordinating the system of ecological and environmental protection for urban agglomerations.