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A coordinated nexus of agricultural resources is vital to achieve food security and sustainable development in China. Comprehensively considering the water-energy-food nexus as well as the external environment, this study adopts a three-stage data envelopment analysis (DEA) modelling evaluation method to assess the agricultural production efficiency (APE) of seven provinces in the middle and lower reaches of the Yangtze River (MLYR) during 1996-2015. The results show that the three-stage DEA modelling evaluation method reveals real APE and is considered to be a better quantitative method than conventional approaches. A gradually widening range of APE is an important challenge for this region. Significantly, this region generates huge demands for agricultural resources. Moreover, regional emissions of greenhouse gases (GHG) decreased from 34.20 million tons standard coal in 1996 to 32.11 million tons standard coal in 2015, though APE has continued to decrease by 2.56% in the past two decades. In general, the management and technology levels should be improved simultaneously, even though specific opportunities for APE improvement vary across provinces in MLYR. However, understanding the temporal and spatial variation of APE along with the WEF nexus from a production-based insight is a vital step toward appropriately targeted policy making for nationwide resources savings and emissions reduction.