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As an important agricultural production area in China, the Yangtze River Economic Belt has a large amount of water resources and rich types of energy. Water and energy resources are the supporting basis of food production, and the production and use of energy also need to consume a large amount of water resources. The three affect each other and are interdependent. Paying attention to the synergistic security of water-energy-food system in the Yangtze River Economic Belt is important for regional economic development. This paper uses the pressure-state-response (PSR) model and selects 27 indicators to build an evaluation index system of the regional water-energy-food system. We use the random forest model to evaluate the security level of the Yangtze River Economic Belt from 2008 to 2017, and the Haken model is employed to identify the driving factors that dominate the synergistic evolution of the system. Then we take the identified factors as the key control variables under each scenario and launch a scenario simulation of some provinces in the Yangtze River Economic Belt in 2025. The results show that due to the improvement of water and energy utilization efficiency and the advancement of agricultural production technology, the level of water-energy-food security in the Yangtze River Economic Belt improved significantly from 2008 to 2017. Each province performs differently in different subsystems, with water resources security being better in the upper reaches and Zhejiang and Shanghai in the lower reaches, and food security being better in the middle and lower reaches. The level of energy security is high in Sichuan, Yunnan, and Guizhou in the upper reaches and Shanghai and Anhui in the lower reaches. According to the results of scenario prediction for Jiangsu Province and Hubei Province in 2025, implementing moderate management in accordance with current management objectives can increase the overall security of the system to level 4. The two provinces should focus on controlling water resources and energy consumption and improving the utilization efficiency of water and energy in agricultural production. Full article