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• Developing a compound flood model that incorporates drainage backflow into urban inundation processes. • Assessing joint probability of compound flood hazards caused by both rainfall and storm tides. • Delineating flood zones by considering the combined impacts of rainfall and storm tide. Low-lying coastal cities are highly vulnerable to compound floods, which may result from a simultaneous occurrence of storm surges and heavy rainfall. Systematic numerical analysis is essential for projecting flood scenarios upon compound events. In this study, a coupled model that integrates the 1D drainage module with the 2D overland flow module is developed and validated by taking Macau as the study area. The joint cumulative probability distribution between rainfall and storm tide are derived based on the historical typhoon data. The flood hazards are projected under designed scenarios, and an investigation is conducted on the backflow processes through drainage system and effectiveness of installing tide gates. The flood zones are delineated and the contributions of rainfall and storm tide to floods are analyzed. Storm surge exerts a greater influence on the maximum inundation depth in the western Macau Peninsula than heavy precipitation does. As the peak tidal level increases from a 10-year to a 200-year return period, the increments of flooded area ratio to the total land area are approximately 19 %. The backflows through underground drainage system could expand the tide affected area during storm events, as indicated by the backflows in the pipe 1.4 km away from the coastal boundary. By installing tide gates, backflows could be greatly eliminated in the corresponding pipes. The inundation area in the compound flood scenario is not equal to the superposition of the extents by the individual components. The transition area that is affected by both storm tide and rainfall extends from coast to inland areas under the combined effects. This study is expected to furnish valuable insights for flood risk assessment, flood hazard prevention and mitigation in low-lying coastal cities such as Macau.