For deep-water long span bridges under earthquakes, the interaction between water and structure will inevitably induce the hydrodynamic force on the structures. Based on the Morison potential fluid theory, a simplified calculation method of hydrodynamic force was proposed. Taken the 3rd Nanjing Yangtze River Bridge in China as the prototype, the shaking table test for the elevated pile caps was performed. And the results from the experiment and the proposed simplified calculation method were analyzed and compared. The main conclusions include: the natural vibration frequency of the bridge in deep water is decreased, and the predominant frequency is reduced by 8.24% due to the water-structure interaction. In earthquake, the effect of hydrodynamic force on the dynamic response of the deep water bridge is significant that the bending moment of the main girder is increased 7.73% and the bottom bending moment of the most adverse pile is increased 14.22%. In the seismic design of deep-water bridges, the effect of water-structure interaction should not be ignored.