Long-period ground motion is easy to cause strong seismic response of isolated structure， which may be more disadvantageous when considering soil-structure interaction （SSI effect）. In order to explore the influence of the SSI effect of the weak interlayer foundation under the long-term period of ground vibration on the dynamic response law and shock absorption performance of the layer interval vibration structure， the numerical simulation and vibration platform test of the single tower layer interval vibration structure of the large chassis on the rigid and soft interlayer foundation are carried out. The results show that the soft interlayer foundation has an obvious amplification and filtering effect on the input ground vibration， which is associated with the peak and spectral characteristics of the ground vibration. After considering SSI effect， the natural vibration period of the structure is larger than that of the rigid foundation， but the extended period multiple of the isolation technology is lower. The SSI effect enlarges the acceleration response to the lower chassis and the diaphragm， and may increase or decrease the acceleration response of the upper tower，depending on the type and intensity of the input seismic vibration. After considering the SSI effect， the seismic response of the isolation structure under long-period ground motions is stronger than that of ordinary ground motions， and the damping effect becomes worse. In particular， the displacement of the isolation layer under near-field impulse ground motions exceeds the limit， the damping effect is poor， and the system fails.