Abstract Coastal cities are increasingly threatened by hurricane‐induced compound flooding. However, the relative contributions of rainfall‐surge interactions and other flood drivers, such as runoff from surrounding rural and local impervious areas, in shaping urban flooding remain unclear. Here, we use a multi‐scale Earth system modeling framework to disentangle the contributions of diverse flooding drivers. The results show that urban flooding is primarily affected by topographic factors (low elevation, flat slopes, and localized flow constrictions), rather than increased runoff from their impervious surfaces. Importantly, runoff from rural areas contributes more to severely flooded urban areas with inundation depth exceeding 1.7 m than local runoff. Although rainfall–surge interactions and sea‐level rise exacerbate inundation along the coastline, over 90% of the compounding effects are absorbed by wetlands. By resolving flooding processes across scales and components, this study emphasizes the role of runoff from surrounding rural areas in shaping zones of severe urban flooding.