<p>Heavy rainfall associated with tropical cyclones over the coastal urban agglomeration in complex terrain involves complicated influences of underlying surface (urban land, topography, and water body), which are not well understood. To investigate these influences, this study takes tropical storm Ewiniar (2018) passing the Pearl River Delta urban agglomeration as an example, and performs several numerical experiments by varying underlying surface using the Weather Research and Forecasting model coupled with the multi-layer urban canopy model (MLUCM). Results show that mountains and urban land combined to maintain the rainfall in the north of the urban agglomeration near the topographic transition region. The urban land enhanced the rainfall over the urban agglomeration mainly through retaining the precipitation system due to increased surface roughness, although the stability and moisture conditions might become less advantageous to extreme rainfall. Besides the blocking effect, mountains acted to accumulate moisture and energy to the south of the mountainous area. Moreover, the interaction between topography and urban land tended to enhance rainfall in the south of the northern mountainous area, while the interaction between urban land and the water body over the Pearl River Estuary (PRE) favored the rainfall to the north of the PRE. The low-level wind speed difference between the downstream area of the PRE and its adjacent urban area resulted in positive vorticity, facilitating convective development. The incorporation of five urban categories and MLUCM in this study also indicates that detailed representation of urban features is important to accurately simulate the fine-scale distribution of rainfall.</p>