Due to rapid urbanization, nutrient-related issues, such as environmental pollution and waste of resources, are now significant in many cities. Urban metabolism is a multidisciplinary concept that focuses on figuring out the energy and various material flows in urban systems. To understand the holistic nutrient metabolism in the context of dynamic and complex town-scale urban systems, energy flow accounting in the discipline of urban metabolism and spatial nutrient flow mapping were applied as major research methods. This research shows the large accounted output nutrient waste and critically discusses the government measurement of decreasing the nutrient pollution from 1986 to 2020 in the case study area, Yuen Long Town, with management strategies proposal, expecting the nutrient can be reused with less output in the urban system after the design input.