This article presents detailed results of a study of the statistical spread of resonant frequencies depending on the power of the layers. A complex multilayer system of interaction between a structure and a soil base, consisting of layers with various physical and mechanical characteristics and geometric parameters, is considered. As part of the study, the simulation of the joint operation of the system elements was carried out and the calculation of the resonant frequencies of the system was performed at different values of the power of the layers. As a result of the study of the “Structure – Multilayer foundation” system, it was found that the power of the layers has a significant effect on the magnitude of the spread of the resonant frequencies of the system. Regression coefficients for the first three resonant frequencies are given, as well as a characteristic type of amplitude-frequency characteristics at different capacities of each soil layer. It is shown that as the power of the layers increases, the spectrum of resonant frequencies thickens. As a result of the analysis of various variants of the addition of the soil base, it became clear that the category of soils significantly affects the amplitude-frequency response of the entire system. The results obtained can be used in engineering practice in the design of earthquake–resistant buildings and structures, in particular, in identifying dangerous resonant frequencies of the “Structure – Multilayer foundation” systems.