The dramatic changes of land-use and cover in the Taihu Basin (TB) during the rapid urbanization process has a profound effect on the spatiotemporal distribution characteristics of water yield. In this paper, we analyze the urbanization process and land-use changes in the TB firstly, and then the TB model is employed to simulate hydrological process for the coupled scenarios of typical rainfall (1991, 1999 and 2009) and land-use (1985, 1995, 2000, 2005 and 2010). Finally, spatiotemporal patterns of water yield changes are revealed synthetically at year, flood season and water-level-rising stage over the whole basin and sub-regions. Temporally, runoff generation growth at all time and space scales present an evident increasing trend with the progress of urbanization and increment further enlarges after 2005. In addition, the annual increase of water yield is mainly concentrated in the flood season. Spatially, the growth rate of all statistical periods in urban cluster over the eastern and central regions significantly exceed that in the western hills and the Taihu region, which is closely related to the less increase of impervious surface percentage over those regions. Spatiotemporal patterns of runoff generation variation obtained from this paper provides crucial prior knowledge for deeply understanding the evolution of basin-region-urban flood control pattern. Moreover, it contributes to scientifically enhance coordination between the three levels of flood control system in the TB with the continuous development of urbanization.