The complex formation mechanism and numerous influencing factors of urban waterlogging disasters make the identification of their risk an essential matter. This paper proposes a framework for identifying urban waterlogging risk that combines multi-source data fusion with hydrodynamics (MDF-H). The framework consists of a source data layer, a model parameter layer, and a calculation layer. Using multi-source data fusion technology, we processed urban meteorological information, geographic information, and municipal engineering information in a unified computation-oriented manner to form a deep fusion of a globalized multi-data layer. In conjunction with the hydrological analysis results, the irregular sub-catchment regions are divided and utilized as calculating containers for the localized runoff yield and flow concentration. Four categories of source data, meteorological data, topographic data, urban underlying surface data, and municipal and traffic data, with a total of 12 factors, are considered the model input variables to define a real-time and comprehensive runoff coefficient. The computational layer consists of three calculating levels: total study area, sub-catchment, and grid. The surface runoff inter-regional connectivity is realized at all levels of the urban road network when combined with hydrodynamic theory. A two-level drainage capacity assessment model is proposed based on the drainage pipe volume density. The final result is the extent and depth of waterlogging in the study area, and a real-time waterlogging distribution map is formed. It demonstrates a mathematical study and an effective simulation of the horizontal transition of rainfall into the surface runoff in a large-scale urban area. The proposed method was validated by the sudden rainstorm event in Futian District, Shenzhen, on 11 April 2019. The average accuracy for identifying waterlogging depth was greater than 95%. The MDF-H framework has the advantages of precise prediction, rapid calculation speed, and wide applicability to large-scale regions.