China has a vast territory and a long history of inland navigation. This paper is based on the Shaying River Shenqiu hub project, and a normal physical model with a geometric scale of 65 was established to simulate the characteristics of water and sediment in the entrance area of the project. By setting different working conditions and measuring and analyzing the velocity flow pattern of the wharf area, planning suggestions for the artificial channel with straight cut-off can be given. Simultaneously, the study simulates the natural sediment deposition state in typical years, observing changes in terrain and evaluating their impact on navigation, thereby validating the rationality of scouring and desilting processes. The research findings indicate that in the reconstructed river wharf’s entrance area, the flow velocity is low, and the flow pattern is stable, ensuring that the transverse flow velocities along the recommended route meet the requirements for vessel navigation. Post-scouring from the regulating gate discharge, downstream deposition decreases, with a sediment flushing efficiency reaching 68.5%. Under the specified conditions, the thickness of sediment deposition after scouring does not negatively affect the water level for ships entering or departing the wharf. The results of this study may offer valuable reference insights for the planning of artificial rivers in similar terrains.