The imbalance of water supply and demand forces many cities to transfer water across basins, which changes the original “rainfall–runoff” relationship in urban basins. Long-term hydrological simulation of urban basins requires a tool that comprehensively considers the relationship of “rainfall–runoff” and the background of inter-basin water transfer. This paper combines the rainfall–runoff model, the GR3 model, with the background of inter-basin water transfer to simulate the hydrological process of Huangtaiqiao basin (321 km2) in Jinan city, Shandong Province, China for 18 consecutive years with a 1 h time step. Twenty-one flood simulation results of different scales over 18 years were selected for statistical analysis. By comparing the simulation results of the GR3 model and the measured process, the results were verified by multiple evaluation indicators (the Nash–Sutcliffe efficiency coefficient, water relative error, the relative error of flood peak flow, and difference of peak arrival time) at different time scales. It was found that the simulation results of the GR3 model after inter-basin water transfer were considered to be in good agreement with the measured data. This study proves the long-term impact of inter-basin water transfer on rainfall–runoff processes in an urban basin, and the GR3-ibwt model can better simulate the hydrological processes of urban basins, providing a new perspective and method.