Based on the Navier-Stokes equations which are set up with the arbitrary Lagrange-Euler description, a finite element model considering close fluid-structure interaction (FST) is established to analyze the seismic response of bridge piers in the deep water. The influence of close FSI on the bridge pier is analyzed including the relative displacement, shear force and bending moment. In addition, the close FSI and its effects are discussed with respect to different water levels. The results of the case study indicate that the displacement and internal force will become larger obviously when the FSI is considered. Effects of the close FSI on seismic response of the pier are related to the frequency characteristics of the input earthquake wave. The larger the peak displacement of input earthquake wave, the larger the FSI effects on the displacement response of the pier are and the smaller the FSI effects on the internal force response of the pier. Additionally, the effect of the water level on internal force response of the pier is more remarkable than that on the displacement response of the pier.