By use of large finite element analysis software, dynamic characteristics analysis is carried out for an aqueduct in South-to-North Water Transfer Project. Westergaard method and Housner method are used respectively to simulate the water. The natural frequencies and mode shapes (wet) of the aqueduct structure are calculated under two kinds of water depths (designed water depth, half water depth). The results show that the influence of the water on the dynamic characteristics of the aqueduct is obvious. Natural frequencies decrease with the increases of the water depth. The distinction between the two methods was analyzed: Housner method is closer to the practical engineering because both the pulsation effect and the convection effect of the water are considered. The results and conclusions can be referenced for seismic design of large aqueduct.