Water, energy, and food are relatively independent yet closely interconnected feedback systems. Frequent extreme weather significantly threatens the security of the water-energy-food nexus. Exploring the impact of extreme weather on the nexus’s security and formulating targeted countermeasures have become the key to achieving sustainable development. Based on system dynamics, this paper constructs a model of the water-energy-food nexus under extreme weather conditions. It predicts the supply and demand of the nexus in Jiangsu Province from 2022 to 2030 under a baseline scenario and different extreme weather scenarios to explore the impact of extreme weather on the collaborative security of the nexus. On this basis, regulatory variables are set from one or both of the supply and demand sides to conduct countermeasure simulation research. The results show that: (1) Under the current trend, the resource supply-demand index of the nexus in Jiangsu Province will show a downward trend from 2022 to 2030. (2) Extreme weather has varying degrees of impact on the security of the nexus in Jiangsu Province. Extreme drought has the most significant impact, followed by extreme high temperatures, and extreme precipitation has the slightest impact. (3) Under extremely high temperatures, countermeasures such as food conservation and reducing energy consumption per unit of industrial added value can most effectively strengthen the collaborative security of the nexus in Jiangsu Province. Under extreme precipitation, countermeasures such as boosting R&D investment and food conservation are the most effective. Under extreme drought, countermeasures such as increasing R&D investment, conserving water and food, and expanding water-saving irrigation areas are more effective.