The research aims to investigate and compare the seismic responses of various models, including free field, pile group, fixed base, and shallow/deep foundation-structure with different structure’s height/width (h/b) ratios in saturated and dry sands during realistic earthquakes with varying intensities to realize the detrimental or beneficial effects of soil-foundation-structure-interaction (SFSI). None of the comparative research has simultaneously considered the shallow/deep foundations response in saturated and dry soil. This paper fills this gap using 3D non-linear parallel finite element models validated with two sets of centrifuge tests, and the extended analysis of nonlinearity effects of seismic SFSI considering large deformation performed. Focusing on the time-frequency content distribution result, the input acceleration amplitudes at different times are intensified by passing through the stiffer system (e.g., dry site, remediated soil, and shorter structure) at high frequencies. However, they decrease in the softer system, especially in liquefiable soil, due to the excess pore pressure build-up. The time of PGA alters at the foundation level, and correspondingly, the commencement time of significant settlement occurs quicker or later. A structure with a higher flexibility base increases rocking and, as a result, reduces flexural drifts, internal forces, and base shear force to seismic weight ratio in the structure, and subsequently decreases the structure's local damage. In contrast to lower h/b, the structure’s base shear force in the saturated soil site is more than in the dry one due to the higher peak structural acceleration. The results need attention in seismic design to help engineers in practical applications.