In this paper, vibration-based methods to monitor damage in foundation-structure interface of harbor caisson structure are presented. The following approaches are implemented to achieve the objective. Firstly, vibration-based damage monitoring methods utilizing a variety of vibration features are selected for harbor caisson structure. Autoregressive (AR) model for time-series analysis and power spectral density (PSD) for frequency-domain analysis are selected to detect the change in the caisson structure. Also, the changes in modal parameters such as natural frequency and mode shape are examined for damage monitoring in the structure. Secondly, the feasibility of damage monitoring methods is experimentally examined on an un-submerged lab-scaled mono-caisson. Finally, numerical analysis of un-submerged mono-caisson, submerged mono-caisson and un-submerged interlocked multiple-caissons are carried out to examine the effect of boundary-dependent parameters on the damage monitoring of harbor caisson structures.