Urban agglomeration has become the main regional unit to cope with global challenges. However, with the development of economic globalisation and urbanisation, urban agglomeration is facing increasing pressure on nature resources and ecological environment. This study takes the Fujian Delta Urban Agglomeration (FDUA) in China as the research area. Emergy analysis theory is used to evaluate the health status of urban agglomeration and its internal cities. Simultaneously, the regional coordination degree model is applied to evaluate the coordination between urban social-economic and resource-environment systems, as well as the coordination among cities. Results show that (1) the FDUA is a consumption-orientated economic system (emergy-based sustainability index < 1), and the social and economic development is dominated by a non-renewable resource input (58.95%) and in a low environmental load state (1.33 < environmental loading ratio < 1.76). (2) The level of urban economic development is characterised by ‘Xiamen > Quanzhou > Zhangzhou’, an order that is associated positively with the demand for external feedback-type emergy, but negatively with the production efficiency of the ecological economy. (3) The regional social-economic and resource-environment systems of the cities in FDUA are moderately uncoordinated states (0.35 ≤ D ≤ 0.4), but the FDUA is generally weakly coordinated (0.52 ≤ D ≤ 0.56). The co-development model of the urban agglomeration is considerably beneficial to the sustainable development of cities. (4) Cross-regional cooperation helps to promote the integration of resource elements and achieve a win–win situation between cities. The research results are intended to serve as an important guide and reference for the FDUA, the Urban Agglomeration on the West Side of the Straits as well as other small and middle urban agglomerations and other ecological civilisation demonstration zones in regulating the intensive use of resources, jointly protecting and controlling the ecological environment and developing cross-regional cooperation.