The extent and depth of coastal flooding caused by tropical cyclone can be underestimated without considering the contribution by storm-induced precipitation. In this study, the dynamic flooding processes in Macau are simulated accounting for the combined effect of storm surge and precipitation during Typhoon Mangkhut in 2018. The surface wind and atmospheric pressure during this typhoon event are generated by a parametric vortex model and are used to drive a surge–tide–wave model for producing storm-induced water levels. The precipitation rate from ERA5 reanalysis data is utilized in this modelling suite as an additional source of water mass. The numerical model is first thoroughly validated by comparing the numerical results against the measured water levels and significant wave heights at tidal gauge and wave buoy stations. By switching on/off the rainfall function in the mass conservation and momentum equations, we compare and analyze the differences of inundation depths and inundation extent induced by precipitation. The differences in the maximum inundation depths vary spatially and the increments owing to precipitation are less than 50 mm in most flooded regions, the associated contribution is less than 10% in areas with moderate and severe flooding. The effect of precipitation as additional rainfall-induced forces in the momentum equations plays a more important role than that in the mass conservation. The inundation depths induced by tide and surge are approximately two times of that induced by precipitation. Moreover, the compound effects by ocean waves and precipitation tend to decrease the increment of precipitation-induced inundation depths by precipitation alone. Finally, we also assess the performance of the overland flow model Itzï on Macau Peninsula for the same typhoon event. The present study helps identifying vulnerable areas subject to heavy precipitation in Macau and gaining more understanding of flooding mechanisms by different physical drivers.