Summary Many basins in Japan are characterized by steep mountainous regions, generating orographic rainfall events. Orographic rainfall may cause localized heavy rainfall to induce flash floods and sediment disasters. However, the accuracy of radar-based rainfall prediction was not enough because of the complex geographical pattern of the mountainous areas. In order to reduce damage due to localized heavy rainfall, characteristics of orographic rainfall must be identified into a short-term rainfall prediction procedure. The accuracy of radar-based rainfall prediction performs best for very short lead time, however the accuracy of radar prediction rapidly decreases with increasing lead times. At longer lead times, higher accuracy QPFs are produced by Numerical Weather Prediction (NWP) models, which solve the dynamics and physics of the atmosphere. This study proposes hybrid blending system of ensemble information from radar-based prediction and numerical weather prediction (NWP) to improve the accuracy of rainfall and flood forecasting. First, an improved radar image extrapolation method, which is comprised of the orographic rainfall identification and the error ensemble scheme, is introduced. Then, ensemble NWP outputs are updated based on mean bias of the error fields considering error structure. Finally, the improved radar-based prediction and updated NWP rainfall considering bias correction are blended dynamically with changing weight functions, which are computed from the expected skill of each radar prediction and updated NWP rainfall. The proposed method is verified temporally and spatially through a target event and is applied to the hybrid flood forecasting for updating with 1 h intervals. The newly proposed method shows sufficient reproducibility in peak discharge value, and could reduce the width of ensemble spread, which is expressed as the uncertainty, in the flood forecasting. Our study is carried out and verified using the largest flood event by typhoon ‘Talas’ of 2011 over the two catchments, which are Futatsuno (356.1 km2) and Nanairo (182.1 km2) dam catchments of Shingu river basin (2360 km2), which is located in the Kii peninsula, Japan.