Taking a large aqueduct in the south-to-north water diversion project as the research object,the paper used the potential fluid element in software ADINA to analyze the dynamic response law of aqueduct structure by considering the fluid-structure coupling interaction.The paper studied the dynamic response of the aqueduct structure under the gateway, two-way and three-way seismic waves respectively. It analyzed the similarities and differences of the two methods such as additional quality standard and scaled complete fluid-structure coupling method of ADINA in the problem of calculating fluid-solid coupling, and the impact of multi-dimensional seismic waves on the dynamic response of structure. Result showed that the water depth and direction of seismic have more influence on the dynamic response of aqueduct structure.It is necessary for us to study the problem of dynamic response under the action of two-way seismic wave.