The Yangtze River Basin is a resource axis represented by hydropower resources, bulk agricultural products, and mining resources. However, with rapid socio-economy development, the balance between water, energy, and food elements in the region has become more fragile. As the core element of the water-energy-food nexus, it is necessary to study water resources security and give effective pre-warning of possible water safety problems from the perspective of water-energy-food symbiosis. In this paper, we introduce the “symbiosis theory” to build a regional water-energy-food nexus symbiosis framework. Then, we establish a Lotka–Volterra symbiotic evolution model to calculate the symbiotic security index. Finally, we judge the water security state and pre-warning level and analyze the causes of water security problems by the inverse decoupling of the indicator-index. The results show that the spatial differentiation of water security in the Yangtze River Basin is obvious from the perspective of water-energy-food symbiosis. The state of water security in the middle and upper reaches of the Yangtze River Basin is better than that in the lower reaches. Specifically, the water resources security levels in the upstream hydropower energy enrichment regions are generally low. By contrast, the water systems of some downstream socio-economically developed provinces have certain risks. Therefore, each province needs to find out the key factors that hinder the healthy development of the water resources system based on combining the evolution mechanism and symbiotic state of water-energy-food so that water security can be managed in a targeted manner.
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