The vibration of a structure system characterizes the system itself and also reflects the variation of the boundary conditions. Therefore, vibration measurement has been widely applied to the system identification and the damage evaluation of structures. In this study, the influence of pier foundation exposure on the vibrational response of the foundation itself and the bridge superstructure were first demonstrated by numerical analysis. Field vibration measurements were made at the Wensui Bridge of Provincial Highway No. 3 to actually investigate the variation of vibration characteristics of the bridge superstructures caused by foundation exposure using the spectral analysis and the vulnerability index. In addition, the bridge unit model of the Wensui Bridge was established to perform the modal analysis and the dynamic time history analysis for the verification of field measurements. All these results showed that the measurement of the vibration of the bridge superstructure can be used to estimate the exposure of the pier foundation.