In order to study the flooding process and the inundation risk it poses to the river basin, GAST, a two-dimensional all-hydrodynamic model, is used to simulate the rainfall flooding in some regions of the Ba River Basin, by which the process of flood formation and the changes of inundation risk area under different rainfall concentrations are analyzed. The results show that rainfall concentration affects the peak flow and peak time of flood in the Ba River Basin, as well as the inundation risk area and its peak time; heavy and concentrated rainfall leads to flooding with large peaks in a short period of time, and also the peak area of the inundation risk. The chronological order of peak time of the mainstream and tributaries of the basin is the Qingyugou, the mainstream of the Ba River, the upper reaches of the Ba River and the Lanqiao River, and the maximum difference of the peak time between the starting point of the confluence and the outlet section of the basin is 80 min. The inundation risk areas mainly distributed along the banks of the mainstream of the Ba River outside the mountain outlet of the river basin, and the earliest peak of inundation area is the low-risk area, the latest is the extremely high-risk area, which occurs before 4 h. The analysis of the flooding process and inundation risk change process of the mainstream and tributaries of the Ba River Basin can provide a reference for the flood response and deployment of control measures under different rainfall conditions in the basin.