[Objective] The situation of sustainable development of ecological-econorng-society system of urban agglomeration along Yangtze River delta were studied in order to support the sustainable development of the ecological economy of the urban agglomeration in this region.[Methods] Based on the emergy theory, the sustainable development of nature, economy and social system of urban agglomeration along the Yangtze River was studied. [Results] In 2017, 29% of the ecological resources were over-exploited, with strong external dependencies, 53% of cities had a low environmental load rate while 29.4% of cities had a high environmental load rate, 11.7% of cities had low waste recycling capacity, 47% of cities had low emergy exchange rates and strong economic competitiveness, 35% of cities had high emergy currency rates, with low economic output efficiency, Shanghai and Suzhou cities had high emergy density per unit area, and 23.5% of cities had lower emergy density, 29.4% of the cities had low per capita emergy welfare, 17.6% of cities had a high population load rate, 41.2% of the cities along the river were sustainable, and 58.8% of the cities were in over development situation.[Conclusion] In 2017, the urban agglomerations along the upper reaches of the Yangtze River were characterized by strong self-sufficiency, low environmental pressure, and excellent ecological quality. The urban agglomerations in the middle reaches coordinated with each other. The urban agglomerations in the lower reaches of the river were characterized by weak self-sufficiency, high environmental pressure, and poor ecological quality. Cities in Shanghai City and Southern Jiangsu Province had strong economic competitiveness, but their output efficiency was low. In Central Jiangsu Province and Central Anhui Province, except for provincial capitals, other cities had weak competitiveness. The economic development of cities in Southern Anhui Province laged behind and isolated along the river. The sustainable development of urban society in Shanghai City and Southern Jiangsu Province was excellent, forming a strong attraction to talents and resources, and they also had the problem of land shortage at the same time. The urban social, economic and ecological development of central Jiangsu Province were relatively balanced, but it had a weak attractiveness to surrounding cities. Except for Hefei City and Tongling City, the overall development of cities in central and Southern Anhui Province lags behind, and there was no effective attraction for surrounding cities. The overall sustainable development of the urban agglomerations along the river was still severe.