A finite element model was developed for solving horizontal seismic response of aqueduct with fluid-structure coupling and pile-soil-structure interaction in this paper. Equivalent linearization principle was employed to deal with the nonlinear characteristics of the soil. Base on the analysis results of free filed, the parameters of viscous-spring artificial boundary and the input method of earthquake wave were given. Analysis was carried out by using this finite element model, the results were in good agreement with the pseudo-dynamic testing data. At the same time, the results of the pseudo dynamic test and finite element calculation show that water has a certain effect on the earthquake response of the aqueduct structure. On the water condition, the fundamental frequency of the aqueduct structure decreases and deviates from the energy basic frequency of the input seismic wave farther than the water-less condition. In this case, it has certain damping effect.