Watershed Cities often face the dual flood risks of upstream floods and urban waterlogging. This compound disaster is caused by the interaction of multiple factors (topography, storms, upstream water and urban drainage, etc.), and is particularly affected by extreme rainfall events and the large and small drainage carrying capacity. To explore the combined effects of extreme rainfall and drainage systems, this study applied the Chicago rainfall hyetograph method and constructed design under different return periods. A comprehensive model combining the verified SWMM and LISFLOOD hydraulic models was utilised to build one-dimensional and two-dimensional coupled watershed urban flood models, simulating inundation depth and duration. By considering urban rainfall, runoff, topography, and drainage system characteristics, the flood processes under different extreme rainfall scenarios were simulated, and the node overflow and inundation depth were obtained. A flood risk assessment of watershed cities was conducted by combining methods such as the HR threshold method, evaluation level, and threshold division. In this study, Huyi District of Xi’an City, China, was used as the research area. The main research findings show: (1) the precipitation design values for different return periods were calculated based on the proposed method, with amount for a 100-year event being 87.196 mm, suitable for composite flood simulation; (2) applying the SWMM-LISFLOOD coupled model constructed for midstream urban areas ensured the accurate simulation of composite flood processes. Under different extreme rainfall return period scenarios, the percentage of flood inundation depth exceeding 1 m caused by multiple disaster factors increased from 0.73 % to 5.19 %; (3) extreme rainfall leads to different levels of internal flooding risk. When the return period of extreme rainfall is 5 years, the area inundated by composite floods in the research area is 67.21 km2. In comparison, when the return period of extreme rainfall is 50 years, the area inundated by composite floods in the research area significantly increases to a total inundation area of 286.85 km2. This study is expected to provide scientific references for flood prevention planning, composite disaster risk management, and urban resilience building in watershed urban areas while significantly impacting modern economic growth, social stability, and the safety of watershed cities.