Taking the Donghaochong Watershed in the typical urban area of Guangzhou City in the Pearl River Delta as the study area, the formula for short-duration rainstorm intensity in the Donghaochong Watershed in the future was derived by combining the Delta method and the annual maximum method. Based on InfoWorks ICM, a one- and two-dimensional coupled urban storm flood model of Donghaochong Watershed was constructed to quantitatively assess the impact of climate change on the drainage system. The results show that under the scenarios of RCP4.5 and RCP8.5, the peak rainfall intensity and the cumulative rainfall in the future will increase. The increases of node overflow, proportion of overloaded pipes and submergence depth of urban drainage system will bring more serious impact to the drainage system. This result indicates that the Pearl River Delta region may suffer more unfavorable flood risk disasters in the future.