Energy–water nexus plays a prominent role in developing sustainable roadmap for cities. The energy-related water and water-demanded energy have been mostly treated as two different aspects from a reductionist way of thinking. In this study, we propose a system-based framework to synthesize the interwoven connections between energy consumption and water use in a city. By taking Beijing as a case study, the energy directly consumed by the city and energy used for water infrastructure are combined and converted into a single hybrid energy inflow to urban nexus network (UNN). Similarly, water directly consumed by the city and water utilized to supply energy are merged in the UNN. The intensities of embodied energy and water triggered by urban consumption are assessed based on input–output model, while the structural properties and sectoral dynamics of direct water- and energy- mediated networks are compared with UNNs based on network analysis. Our findings show direct and embodied energy/water consumptions are distinct in terms of the sectoral configuration. The recycling rates in water networks are around 22–23%, which are lower than those of energy networks (28–29%). The robustness of water and energy networks approximates the values of oil network and iron and steel network but is lower than that of natural ecosystems in general. The control/dependence relationships between sectors are altered significantly due to urban nexus, and the effect of nexus on water network (±30%) is smaller than energy networks (±200%). The network approach presents a great potential of bridging nexus analysis with sustainable urban planning by simultaneously addressing energy and water challenges.