The energy–water nexus in urban activities poses challenges for coordinating urban energy and water management. A difficulty in such nexus issue is the lack of a unified base for energy and water flows analysis, which hinders sustainable energy and water resource utilization. Given that, we proposed a modified input–output analysis to provide a unified framework to balance urban energy and water use, by using the case of China’s capital city–Beijing. First, we inventoried the energy–related water consumption and water–related energy consumption with emergy metric. The hybrid water flow, as the sum of the direct water flow and energy–related water flow, is combined with the hybrid energy flow to build the hybrid network. Then the complex interactions between economic sectors and the nexus impacts were explored via input–output analysis. The results show that Manufacture (Ma) provides the largest outflow of hybrid energy, and Agriculture (Ag) is the largest receiver. The major export–import pairs of hybrid water are Ag–Ma, Ma–Co (Construction), Service(Se)–Transportation and Mailing (Tr), Ma–Se, and Tr–Ma. These major export–import pairs (Ma–Ag) as well as Ma itself are the critical points for energy and water nexus management. The results of the nexus impacts showed that Ag, Tr, and Co are the most important sectors. This study may help identify the leverage points and regulating pathways of urban energy–water system and provide a better way for mitigating the urban energy and water pressures.