In order to study the underground structure under the action of an earthquake, the relationship between the displacement and the stress between layers of different soils under the action of the earthquake was carried out through the finite element numerical analysis software. The influencing mechanism of soil layer depth on the seismic response of underground structure was discussed, and the seismic response law of the system was worked out. The research results indicated that the displacement response of the soil layer structure in three directions depicted obvious laws with the change of soil layer depth. There were evident similarities and differences in the response of soils with different properties to seismic responses. These conclusions provided a certain reference for the seismic design of underground structures.