The minimum distance between the piers of the proposed Nanjimen track-specific bridge and the downstream regulation buildings is only 24 m. The completed piers will have a certain adverse impact on the stability of the regulation buildings themselves, which can affect the waterway regulation effect of this river section and the realization of the established regulation goals. We use the two-dimensional flow and sediment mathematical model to calculate the changes of water and sediment conditions after the completion of the bridge piers, and analyze the effect of the proposed joint protection scheme. The results show that the bridge construction has little impact on the navigable flow conditions of the channel in engineering river section. However, it will cause local scour in areas such as the pier, the front of the vertical retaining wall and the head of the spur longitudinal dike, which can affect the stability of the pier, the retaining wall and the Z1# spur longitudinal dike itself. After the implementation of the joint protection scheme, the local scour range is significantly reduced, and the scour intensity is significantly weakened, which ensures the stability of the regulation buildings and bridges, and ensures the normal functioning of the original design function of the channel regulation project.