Soil–structure interaction (SSI) leads to a modification in the dynamic properties of structure, but due to the complexity of analysis, it is traditionally assumed in seismic designs that the structure is fixed-supported on the ground, which brings about potential risks to the seismic performances of structure. The study works on the possibility of SSI having detrimental effects by comparing the dynamic responses of the SSI system to a fixed-base structure, and presents charts for an evaluation of the system frequency of SSI for the purpose of engineering practice. In order to reveal the physical nature, the SSI model is reduced to its simplest form, consisting of a SDOF oscillator, a three-dimensional rectangular foundation, and a multi-layered half-space. The energy dissipation in the soil is achieved by foundation impedances and the substructure method. Previously, the foundation impedances are usually acquired by two-dimensional or axisymmetric three-dimensional models in uniform half-space to avoid the high cost of the more realistic, fully 3D models, while a high-precision indirect boundary element method is employed, combined with the non-singular Green’s functions of distributed loads to calculate the foundation impedances. Although SSI dampens the peak amplitude of structure response in the frequency domain, case studies on four buildings’ responses to 42 earthquakes in the time history show a possibility of 15–20% that SSI amplifies the dynamic responses of structures, such as the maximum and the mean values in the time history, depending on the properties of the structures and the site, as well as the frequency component of incident waves.