Purpose - Urban agglomeration construction is one of national strategic plans to accelerate the development of industrialization and urbanization in China, which has threatened the eco-environmental quality at the same time. This paper selected the urban agglomeration in the middle reaches of the Yangtze River as the research area. Research design, data, and methodology - The the slack-based measurement (SBM) model considering undesirable outputs is applied to measure the eco-efficiency of this urban agglomerations during 2006-2015. Results - The empirical results show that average eco-efficiency of the urban agglomeration in the middle reaches of the Yangtze River is 0.595. Regional ecological development is unbalanced. The highest eco-efficiency is recorded at Wuhan Metropolitan Area, and the lowest one is at the Changsha-Zhuzhou-Xiangtan City Group. Energy consumption and waste dust emissions are the key factors led to ecological inefficiency. Based on this, potentials for energy saving and waste dust reducing are calculated. Conclusions - Finally, this study provides policy implications targeted to promote the coordinating development of economy and eco-environment under the construction of urban agglomeration.