The waterlogging disaster has become a major threat to the resilient development of cities, which needs a unified and systematic accounting framework to estimate potential waterlogging effects in terms of forming disaster prevention strategies. In this paper, we developed an emergy-based waterlogging footprint accounting framework applying depth-damage functions, input–output (IO) analysis and ecological footprint, considering both economic and environmental factors. Taking the old town Beijing as a case study, we simulated the urban waterlogging distribution with a hydrodynamic model (InfoWorks ICM) over different return periods (1, 2, 3, 5, 10, 20, and 50 years) at high resolution. This study first considered the economic impact caused by urban waterlogging to evaluate the direct economic loss and indirect economic loss by using the depth-damage function and IO model, respectively. The environmental loss was assessed with an ecological footprint and was unified by emergy with economic loss. Then, four emergy-based indicators were established to quantify the specific impacts of waterlogging on urban resilience. The results show that the waterlogging footprints grew constantly by 284.57% from 1 year to 50 years. The waterlogging footprints driven by environmental loss, which were overlooked, accounted for 13.02% of the total. The waterlogging footprint density and waterlogging resilience index showed high spatial heterogeneity, indicating that the sensitivity of subdistricts to waterlogging varies greatly. Our study provides a useful energy-based tool for assessing urban waterlogging losses and supports decision-making for waterlogging disaster mitigation and risk zoning management.