In order to explore the law of compound flooding under different encounter scenarios of extreme storms and spring tides, combined with multidisciplinary atmospheric model, oceanographic numerical model and coupled onedimensional and twodimensional hydrodynamic model, a modelling framework of compound flooding integrating atmosphere, ocean and city was proposed to simulate the complete processes of typhoon, rainstorm, storm surge, flood inundation, etc. Considering various scenarios in which the peak of storm surge during Typhoon Mangkhut in 2018 just encountered the lowest (S1 and S5 scenarios), middle (S2 and S4 scenarios) and highest (S3 scenario) levels of spring tide happened in June 2022 in the Pearl River Estuary, the flood inundation changes in the northern part of Hengqin Island, Zhuhai were analyzed. The results show that the inundation area, inundation depth, and flood volume present the law of S3＞S4＞S2＞S5≈S1, indicating that the scenario in which the peak of storm surge encounters high level of spring tide is more likely to cause severe compound flooding. As the maximum total water level rises, the dominant factor of compound flooding will change from the node flooding of drainage system to the inundation caused by seawater. There may also be significant differences in the compound flooding under similar concurrent scenarios (such as S2 and S4 scenarios), indicating that storm surge and spring tide encountering in different phases may have a significant impact on compound flooding.