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Taking a representative catchment of the Yangtze River Delta region as the study area, this research evaluated sub-daily rainstorm variability and its potential effects on flood processes based on an integrated approach of the HEC-HMS model and design storm hyetographs. The results show that the intensities of rainfall on sub-daily scale are getting more extreme. The annual maximum 1-, 2- and 3-hour rainstorms followed significant upward trends with increases of 0.32, 0.43 and 0.44 mm per year, respectively, while the annual maximum 6-, 12- and 24-h events had non-significant rising trends. The detected significant trends in short-duration rainstorms were then used to redesign storm hyetographs to drive the HEC-HMS model, the results show that these changes in short-duration rainstorm characteristics would increase the flood peak discharge and flood volume. These findings indicate that regional flood control capabilities must be improved to manage the adverse impacts of rainfall variation under changing environments.