As the top of the pile foundation in high-pile wharf is connected to the superstructure and most of the pile bodies are located below the water surface, traditional damage detection methods are greatly limited in their application to pile foundation in service. In the present study, a new method for pile foundation damage detection is developed based on the curve shape of the curvature mode difference (CMD) before and after damage. In the method, the influence at each node on the overall CMD curve shape is analyzed through a data deletion model, statistical characteristic indexes are established to reflect the difference between damaged and undamaged units, and structural damage is accurately detected. The effectiveness and robustness of the method are verified by a finite element model (FEM) of high-pile wharf under different damage conditions and different intensities of Gaussian white noise. The applicability of the method is then experimentally validated by a physical model of high-pile wharf. Both the FEM and the experimental results show that the method is capable of detecting pile foundation damage in noisy curvature mode and has strong application potential.