Taking the Kowloon Peninsula of Hong Kong in the Guangdong-Hong Kong-Macao Greater Bay Area as the study area, considering the urban terrain, buildings, and drainage network elements, a waterlogging disaster model under the superposition of storm surge and extreme rainstorm was constructed, and a variety of waterlogging prevention and control methods were quantitatively evaluated. The results show that the waterlogging disaster model can accurately reflect key physical quantities such as the extent of inundation and water depth at different locations. Check valves and baffles can weaken the amplification effect of storm surges on urban waterlogging by cutting off seawater backflow channels. Under the superposition of a 1 000 a return period storm surge and extreme rainstorms, the overflow rate of the pipeline network decreases by 14.8% and the net drainage volume increases by 5.7% after the addition of check valves in area near Yenchow Street, Shamshuipo, West Kowloon. The addition of a 1 m baffle at Container Terminal No. 8 reduces the inundated area by 26%. Underground flood storage ponds reduce the level of inundation around the perimeter by pooling and storing surface runoff, which reduces the inundation of the Boundary Street Playground by up to 34% under the condition of a 100 a rainfall return period rainfall event.