The storm surges caused by tropical cyclones may lead to overtopping floods in low-lying coastal communities, which will be further exacerbated by sea level rise. In this study, a numerical model is developed that can simulate the two-dimensional surface flow and one-dimensional drainpipe flow simultaneously. Then this model is validated and applied to Macao Peninsula. The compound flood scenarios of storm surge and sea level rise are therefore forecasted, with storm surge return periods of 5-, 10-, 20-, 50-, 100-, and 200-years, and sea level rises by 0 m, 0.5 m and 1.0 m. The overtopping floods caused by storm surges are mainly distributed in the west and northwest of Macao Peninsula. When the sea level rises by 1.0 m, the backflow occurs 2 h earlier than that does under the current sea level. Adding pumping station can reduce backflow and improve drainage efficiency significantly. The effectiveness of the drainage system during floods can be quantified using backflow coefficient and drainage efficiency coefficient, which both decrease as the storm tide level increases. In the worst-case scenario of 200-year-return-period storm surge and 1-m sea level rise, the flooding area accounts for 41.1% of the land area, and the population at risk reaches 68.4% of the total population. The storm-surge-prone area overlaps with densely populated area in western Macao Peninsula, where the effects of storm surge and sea level rise are intensified.