<p>To reveal the hydrodynamic mechanisms of ship navigation through the bridge of inland waterways, this study adopts a Computational Fluid Dynamics (CFD) approach based on an overset mesh technology to simulate the entire process of an integrated hull-propeller-rudder self-propelled ship passing through a bridge pier. Unlike traditional studies based on towing conditions or simplified propulsion models, the coupling effects of self-propulsion and shallow water are incorporated within a unified framework. Unsteady hydrodynamic responses during pier passage are analyzed, with emphasis on the viscous flow structures around the hull and the evolution of propeller-induced vortices. The results show that the lateral force has a typical “pus-suction-push” pattern, with peak suction increasing by about 70% in shallow water compared with in deep water, resulting in increased lateral instability. The lateral moment coefficient has three significant peaks, with the maximum occurring near the pier. The pier wake is found to partially mitigate the increase in ship resistance caused by shallow water. In addition, the pier-induced flow disturbance leads to a significant breakdown of the propeller tip vortex system, resulting in a reduction of propeller thrust by about 40% and a corresponding decrease in propulsion efficiency. This study provides new insights into the unsteady interaction between ships and piers by clarifying the coupling of self-propelled forces, shallow water effects, and pier induced disturbances, as well as a practical reference for the safety of maneuvering in bridge areas of inland waterways.</p>