The dynamic response of underwater structures is different from those in air because of interaction between fluid and solid. The influence of water depth on dynamic effect of the pier is studied base on a cable-stayed bridge in deep water. The girder of the cable-stayed bridge is simplified as a lumped mass on the top of the pier. The three-dimensional finite element models of pier with different water levels are built to calculate the dynamic characteristics and dynamic response of the pier under the action of harmonic load. The calculated results show that with the rise of water level, the nature frequencies of the pier decrease while the displacement and stress increase.