Urban metabolism analyzes the supply and consumption of nutrition, material, energy, and other resources within cities. Food, water, and energy are critical resources for the human society and have complicated cooperative/competitive influences on each other. The management of interactive resources is essential for supply chain analysis. This research analyzes the food-water-energy system of urban metabolism for sustainable resources management. A system dynamics model is established to investigate the urban metabolism of food, water, and energy resources. This study conducts a case study of Shihmen Reservoir system, hydropower generation, paddy rice irrigation of Taoyuan and Shihmen Irrigation Associations, and water consumption in Taoyuan, New Taipei, and Hsinchu cities. The interactive influence of the food-water-energy nexus is quantified in this study; the uncertainty analysis of food, water, and energy nexus is presented.