After coupling long-period seismic motions with the soil–structure interaction (SSI) effect, isolated structures can easily be resonated, and the seismic response of the structure is significantly enhanced. The SSI effect can alter the dynamic characteristics of a structure, resulting in a deviation between the assumed seismic-isolation effect of the rigid foundation and the theoretical results. To investigate the dynamic characteristics and seismic-response laws of interlayer structures considering SSI under long-term seismic motion, four types of ground motions (near-field ordinary, far-field ordinary, near-field pulse, and far-field harmonic ground motions) were selected, and two structural models (rigid-foundation and soft soil foundation interlayer seismic-isolation structure models) were established. Experiments were conducted using a combination of shaking-table tests and finite-element simulations. The results show that the use of the SSI effect caused the decrease in the acceleration response of the upper structure of both models under four types of seismic motions and increased the seismic peak ground acceleration (PGA). In addition, the weakening of the acceleration response of the upper structure under ordinary seismic motion is significant for longer periods of seismic motion. Furthermore, when considering the SSI effect, the displacement response ratio under long periods and ordinary ground motions is greater than that of rigid foundations, and the horizontal deformation of the isolation layer under long-period ground motions is greater than that under ordinary ground motions. This shows that the SSI effect weakens the interlayer shear force under ordinary seismic action more than that under long-period seismic action. When PGA increases, the interlayer shear force response of the interlayer isolation structure model with a soft soil foundation under a long-period seismic action may be smaller than that of the rigid-foundation model.