Nondestructive and rapid damage detection method of pile foundation in high-pile wharf is a research hotspot in engineering field. In this paper，we design a dynamic damage detection mode，and study the applicability of modal flexibility in damage detection of the pile foundation in high-pile wharf through a finite element model（FEM） simulation and a physical model test. The results show that：1）The modal flexibility can accurately detect the location of the damage in finite element simulation. The greater the damage degree，the greater change of modal flexibility.The variation of modal flexibility can qualitatively reflect the damage degree of the structure. 2）The modal flexibility obtained based on the physical model can reflect the damage location，but the damage detection effect is not as good as that in the FEM simulation due to the existence of noise and test error，and the damage degree cannot be reflected. The extensive application of modal flexibility damage detection of pile foundation in high-pile wharf needs further development of dynamic testing technology and modal analysis technology.