The Ningxia reach of the Yellow River (NRYR) is wide and shallow, and instability and damages are likely to occur at its vulnerable zone. In this study, based on the one‐dimensional hydro‐sediment dynamics, two‐dimensional hydro‐sediment dynamics and vulnerable zone stability analysis model, a coupled model was established to analyze the scouring risk of the vulnerable zones in the NRYR during flood season. Considering the morphological change of bank slope at the vulnerable zones caused by flow erosion, the seepage stability of a typical spur dyke and protection embankment under the water level fluctuation conditions was analyzed. To fully reflect the coupled scouring effect of flow and sediment, the water flow scouring intensity index α is proposed. A significant increase of water flow scouring intensity index α will result in bank toe scouring, while its significant decrease will lead to silting of the bank toe. The probability of instability failure of the bank for the spur dyke slope is greater during the flood recession period. Compared with the influence of the change of river water level in the flood season, the slip stability of the bank slope is more sensitive to the change of bank toe erosion.