To study the variation law of the response of silo-shaped parking garages under the seismic action, vibration table tests and numerical simulation methods were employed. The effect of seismic waves with different incident directions, peak accelerations, and loading frequencies on the seismic response of the structure was analyzed by monitoring the stress distribution, displacement, deformation response, and acceleration of the structure. The results show that the stress concentration areas remain unchanged under different incident directions. When the horizontal seismic wave acts, the response of the structure in the horizontal direction (the direction parallel to the ground) is greater than that in the vertical direction (gravity direction), while when the vertical seismic wave acts, the opposite is true, and the vertical response of the floor slab is obvious. The horizontal-vertical coupled seismic wave intensifies the vibration of the soil and increases the structural stress. The change of peak acceleration does not cause a change in stress distribution, but will make the stress concentration phenomenon more significant. When the frequency is too high or too low, the change of radial stress is not significant. Overall, the stress mainly concentrates at the joints between the cylinder wall and the bottom plate, as well as those between the columns and the floor slabs, which are the key areas for aseismic design.