Change of the environment, namely climate change and human activities, is influencing hydrological cycles globally. Nonstationary changes have been widely detected in precipitation series, which has significantly increased the flood risk in various areas. Taking Taihu Basin as the typical study area, the nonstationary characteristics of precipitation are analyzed through the Mann-Kendall trend test, Pettitt abrupt change test, Sen’s slope estimator and Seasonality Index in this study. Spatial distributed daily precipitation data during 1979–2017 is used. An 1D-2D coupling hydrodynamic model is built by MIKE Zero to simulate the change of flood risk under the nonstationarity of precipitation. According to the results of statistical analysis, the precipitation of Taihu Basin shows increasing trends in various temporal and spatial scales. Especially, the torrential rain and extreme precipitation, which are the main cause of flood disasters of the basin, are increasing significantly especially in highly urbanized areas such as Shanghai city. According to simulation results, the increase of flood risk shows high correlation with the nonstationary change of precipitation. The results indicate a great impact of climate change and urbanization on the regional flood risk, which must be well solved during social and economic sustainable development.