The coupling between water and buoys in ship lift system under earthquake loading is a difficult problem affecting ship lift safety operation.Using fluid dynamics simulation (CFD) method,we discuss the water oscillation in the shaft of ship lift at different frequencies of sine excitation.The result shows that there exists a natural frequency of water in the shaft,which is greater 10% than the one of the rectangular pool with the same size and the same water depth,the natural vibration period is about 0.42s.The natural frequency of shaft water basically does not change with height.