Abstract: Significant sediment siltation exists beneath certain high-pile wharves in China, which was not accounted for in the initial design. This sediment siltation, combined with vessel collisions, results in a coupling effect on the stress experienced by the pile foundation. A 3D finite element numerical model was established to simulate the interaction between vessel collisions, superstructures, pile foundations, and soil, analyzing the effects of sediment siltation and vessel impacts on pile foundation stress in high-pile wharves. The results indicate that the maximum principal stress, shear force, and bending moment at the pile tops in areas of severe sediment siltation significantly increase compared to pre-siltation conditions, highlighting the critical influence of sediment on pile foundation stress. For vessel collision velocities of 0.1 and 0.2 m/s, the impact of vessel collisions on the pile foundation is less significant than that of the sediment siltation. Variations in stress are observed between different bent frames of the wharf, with the pile foundation tops behind the wharf being most vulnerable, where the bending moment approaches the cracking moment of the concrete, increasing the risk of damage and cracking in the pile foundation.