Coastal cities are affected by the compound effects of flood hazard systems, including the ocean, river, and coastal land, within which the disaster-induced factors interact complexly. To explore the combined effects of multiple disaster-causing factors under changing environment, this study first constructed univariate distribution by maximum daily precipitation of the year at Zhuhai Station from 1962 to 2020 and maximum daily average river discharge of the year at Makou Station from 1951 to 2005. Based on the integrated model of the validated Delft3D-FLOW and HEC-RAS hydrodynamic models, the river level process of compound floods was simulated for 24 h, and the effects of extreme compound flood events involving storm surge, rainfall and river flood under future scenarios is analyzed. In this study, the Modaomen waterway in Zhuhai City of China is used as the study area. The results show: (1) The Lognormal distribution is selected as the optimal distribution, and the design values of precipitation and discharge in different recurrence periods are calculated based on Lognormal distribution. The precipitation and discharge for the 100-year return period were 450.3 mm and 51000 m3, respectively, which could be used in the compound flood simulation; (2) The application of Delft3D-FLOW model ensures the accurate simulation of the compound flood process. In the different future scenarios of rising sea levels and increasing wind intensity (WI), the effect of multiple disaster-causing factors results to a more serious inundation than that of a single disaster-causing factor, with the increase of maximum storm surge level from 8.09 % to 20.31 %; and (3) Fluvial flooding and storm surge became the major causes of compound flood when the city coastal protection is vulnerable, while in the city with robust coastal protection, precipitation serves as a main disaster-causing factor. Taking the inundation under scenario S1 as an example, when the seawall elevation is 2 m, the composite flooding causes significant inundation in the riparian area (the total inundation area is 15.29 km2), whereas when the seawall elevation is raised to 2.5 m, the inundation area in the riparian area caused by the compound flood decreases significantly (the total inundation area is 0.03 km2). This study is expected to provide scientific references on disaster prevention planning, compound disaster risk management and urban resilience construction along the coastline, as well as have a significant impact on modern economic growth, social stability, and the security in coastal cities.