With the acceleration of urbanization in a river basin, the changes in the underlying surface structure of the basin are more and more intense, which causes frequent floods. This article aims to analyze the applicability of the HEC-HMS model in flood simulation in urbanization basins and the influence of land use changes on catchment runoff. Pu River Basin is a typical urbanization basin and is taken as the research project. Based on land use changes, soil types, and long-term hydrological data in the Pu River Basin, the HEC-HMS hydrological model is constructed using GIS and HEC-geoHMS. Then, the relative error of flood peak and runoff, Nash–Sutcliffe efficiency coefficient, and correlation are used to evaluate the model simulation rating. The results show that the HEC-HMS model is suitable for an urbanization basin, and its performance grade before urbanization is better than that after urbanization. Finally, sensitivity analysis of nine parameters on model performance shows that curve number, initial abstraction, imperviousness, and time lag are the main parameters. The research results will provide a reference for urbanization basins’ flood simulation and stormwater management.