In port dock engineering, high-piled wharves represent one of the primary structural forms. Damage to the foundation piles is a common issue, influenced by external loads such as impact forces during vessel berthing, slope deformations, and operational loads. This study focuses on the Jungong Road Wharf in Shanghai, utilizing FLAC 3D version 6.0 to conduct dynamic calculations under ship impact loading. The dynamic responses of the structure were analyzed, and various internal forces were extracted during the impact event. By combining concrete cracking failure criteria and fatigue damage theories, the effects of ship collisions on the cracking damage of high-piled wharf structures under different scenarios were assessed. Additionally, the applicability of modal flexibility in high-piled wharf scenarios was evaluated through finite element simulations. The results indicate that the dynamic amplification factor caused by dynamic loading is approximately 1.5, underscoring the necessity of considering this effect in the design and impact analysis of high-piled wharves. The impact loading significantly influences the bending moments of the piles, with inclined piles showing the greatest sensitivity. When a designed ship model collides with the high-piled wharf structure at a speed of 0.2 m/s, the tensile stress in the inclined piles reaches 87% of the ultimate tensile strength of the reinforcement. The impact loading has a relatively minor effect on the axial forces of the piles, a limited influence on the bending moments of the beams, but a considerable impact on the axial forces of the beams. Berthing by oversized vessels and unexpected incidents can lead to more severe damage to high-piled wharf structures. In the finite element simulations, modal flexibility effectively identified the locations of damage, with greater changes in modal flexibility correlating with increased damage severity.