Abstract: For safety appraisal of an aqueduct, an ANSYS three dimensional finite element model of a single span aqueduct structure has been developed with design water level and without water. The fluid solid interaction Housner model is selected to simulate the interaction between water and the aqueduct wall and different pier heights of the aqueduct are set: 8.3 m, 10.3 m, 12.3 m, 14.3 m respectively. The dynamic response of the aqueduct structure under different pier heights (stress, displacement, velocity) based on modal analysis and dynamic analysis is observed. Analysis results show that the natural vibration frequencies of the aqueduct structure under the design water level are less than those without water. With increase of the pier height of the aqueduct, the frequencies of the structure show the trend of decrease; the dynamic response values of the key points of the top of the pier, the mid span and the top of the mid span have the tendency of increase; however, the dynamic response values of the different position of the aqueduct structure are different, therefore, the dynamic response values of the high pier aqueduct is generally greater than that of the short pier aqueduct under the practical conditions of earthquake.