Taking the project of Baihetan large gear-rack vertical ship lift for example，according to different machine room types of ship-lift scheme，we establish a 3D finite element model of the large vertical ship-lift tower structure model which considers the interaction of foundation-tower-top machine room using finite element analysis software ANSYS，calculate the displacement and acceleration responses of the ship-lift tower and top machine room adopting the time-history analysis method，and compare the seismic response and whipping effect under different working conditions. The results show that the first mode of the tower structure is transverse vibration and the second is torsional vibration，and it is necessary to strengthen the torsional stiffness of the structure properly in the design of the tower structure. The whipping effect of large vertical ship-lift is obvious under the seismic action，and the separate machine room is more advantageous than the integrated machine room in whipping effect. The type of machine room should be selected reasonably when designing the ship-lift structure，and the top of the tower should be connected with a beam-slab structure.