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 structural height-to-width ratios (h/b) in saturated and dry sands during realistic earthquakes with varying intensities to ascertain whether soil-foundation-structure-interaction (SFSI) has beneficial or detrimental effects. To date, no comparative research has considered the response of shallow and deep foundations in both saturated and dry soil simultaneously. This study addresses this gap using 3D non-linear parallel finite element models validated with two distinct 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. Conversely, they decrease in a 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 more flexible base exhibits greater rocking and a reduction in flexural drifts, internal forces, and base shear force to seismic weight ratio. This subsequently results in a decrease in the local damage sustained by the structure. In contrast to lower h/b, the structural base shear force in the saturated soil site is greater than in the dry one, due to the higher peak structural acceleration.