Increasing resource crises force cities to scrutinize resilience status of urban food-energy-water (FEW) nexus system, which is highly depend on their metabolic processes. Taking Megacity Beijing as the case, we developed an ecological network model to explore structural and functional characteristics of urban FEW metabolic systems, with consideration of local availability, cross-region supply and resource nexus. The results show that the metabolism of food, energy and water exhibits different topological structures, and water presents typical loop network structure with APL and FCI values of 3.02 and 0.08 respectively, while food metabolizes in a loose topology and energy suffers dissipative losses in a uniflow form. This makes water metabolic network a robust organization with greater circulation, higher stability index (1.81) and better adaptive capacity to counter to vulnerability, yet energy network performs poorly for lacking redundancy and food network is more sensitive to changing conditions. Our findings enable decision-makers to find opportunities to build a more resilient city via improving FEW metabolic network synergistically, such as strengthening local resource reserves to provide buffering capacity when external supplies fail, as well as enhancing utilization efficiency of dominant industries and promoting treatment and reuse to make continuous survival and prosperity possible.