This study aims to evaluate the change in flood inundation in the Chitose River basin (CRB), a tributary of the Ishikari River, considering the extreme rainfall impacts and topographic vulnerability. The changing impacts were assessed using a large-ensemble rainfall dataset with a high resolution of 5 km (d4PDF) as input data for the rainfall–runoff–inundation (RRI) model. Additionally, the prediction of time differences between the peak discharge in the Chitose River and peak water levels at the confluence point intersecting the Ishikari River were improved compared to the previous study. Results indicate that due to climatic changes, extreme river floods are expected to increase by 21–24% in the Ishikari River basin (IRB), while flood inundation is expected to be severe and higher in the CRB, with increases of 24.5, 46.5, and 13.8% for the inundation area, inundation volume, and peak inundation depth, respectively. Flood inundation is likely to occur in the CRB downstream area with a frequency of 90–100%. Additionally, the inundation duration is expected to increase by 5–10 h here. Moreover, the short time difference (0–10 h) is predicted to increase significantly in the CRB. This study provides useful information for policymakers to mitigate flood damage in vulnerable areas.