The “Water-Energy-Food Nexus” is one of the present research hotspots in the field of sustainable development. Water resources are the key factors that limit local human survival and socioeconomic development in arid areas, and the water footprint is an important indicator for measuring sustainable development. In this study, the structural dynamics and complex relationships of the water-energy-food system in arid areas were analyzed from the perspective of the water footprint, and the risk characteristics were evaluated. The results show that: (1) Agriculture products and livestock products account for the largest water footprints (>90%), which is much higher than the water footprints of energy consumption (<5%). From the water footprint type, the blue water footprint (>50%) > the grey water footprint (20%–30%) > the green water footprint (<20%). (2) Since 2000, especially after 2005, while energy consumption drove rapid economic growth, it also led to the rapid expansion of the water footprint in the Manas River Basin. By 2015, the water deficit was relatively serious, with the surface water resource deficit reaching 16.21 × 108
. (3) The water-energy risk coupling degree of the water-energy-food system in this basin is comparatively significant, which means that it is facing the dual pressures of internal water shortage and external energy dependence, and it is vulnerable to global warming and fluctuations in the international and domestic energy markets. Thus, it is necessary to adjust the industrial structure through macroeconomic regulation and control, developing new energy sources, reducing the coupling degree of system risks, and achieving sustainable development.
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