Rapid urbanization and climate change have heightened urban flood risks. An in-depth examination of the underground drainage pipe network’s effect on urban flood inundation can enhance urban stormwater management and mitigate disaster risks. This study presents a full hydrodynamic urban flood model (FHUM) coupling the pipe transport module of the Storm Water Management Model (SWMM) with a shallow water model. Based on unstructured grid cells, runoff yield and confluence calculations are carried out to effectively separate the underground drainage pipe network from other factors. The model is applied to Minzhi Area and Haidian Island to quantitatively assess the influence of the underground drainage system on urban flooding. Results indicate that FHUM performs well, accurately reflecting the process from rainfall to inundation. The underground drainage pipe network reduces surface inundation in the study area and improves the city’s stormwater drainage capacity. With increasing rainstorm intensity, the impact of the pipe network does not exhibit a consistent trend. During heavy rainstorms, the pipe network consistently plays a significant and stable role, particularly in reducing high inundation depths. However, attention should be paid to the potential flood risk transfer associated with using pipe networks in urban flood management. This work provides a scientific basis for urban stormwater management, holding significant importance in improving flood control and disaster reduction capabilities.