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One major threat to cities at present is the increasing rainstorm waterlogging hazards due to climate change and accelerated urbanization. This paper explores the mechanism of rainstorm waterlogging and enables the fine simulation of surface water propagation over complex urban terrain. A novel community-scale waterlogging modeling scheme is presented by loosely coupling a one-dimensional sewer model with a two-dimensional overland model under an open-source framework. The coupled model was applied to Waigaoqiao Free Trade Zone located in Pudong New Area of Shanghai. To quantify the influence of rainfall intensity and drainage conditions on the waterlogging, 12 scenarios were constructed by combining four rainfall return periods (3, 5, 10, and 20 a) and three startup water depths (1.5, 2.0, and 2.5 m) of pump stations. The multi-scenario simulation results show that the waterlogging risk increases from north to south in the study area, and that risk zones with water depth above 0.3 m are mostly concentrated in the southwest and southeast corners of the site. The longer the rainfall return period, the larger the submerged area, and the spatial distribution of surface water accumulation is affected by local topography and drainage system. In addition, reducing the startup water depth of pump stations has an obvious effect on inhibiting the severity of water accumulation. The results provide insights into overland flow across an urban area with densely populated buildings and help to reduce the risk of rainstorm-induced waterlogging disasters.