The aim of this study is to consider the effects of the variation of shear modulus ratio (G/G0) and damping ratio (ξ) of soil, obtained by a linear iterative method based on the design spectra of seismic codes, the soil environment in terms of uncertainties in shear modulus using Monte Carlo simulations and the foundation damping (ξf) of flexible base for analyses of the Soil-Structure Interaction (SSI) problems. A squat structure with circular shallow foundation resting on a soil layer over a homogeneous half-space is studied by using cone model and considering seismic zone effect on structural response. Firstly, after showing the effects of the correction of G and ξ on impedance functions and the responses of soil-foundation-structure system, a study is carried out to compare these effects to those of the modelling of uncertainties in shear modulus as random variations. Secondly, a comparative analysis on design response spectra and base shear forces was carried out for four seismic codes (Algerian Seismic Rules RPA99-2003, Eurocode 8–2004, International Building Code IBC-2015 and Indian Code IS-1893-2002) considering the three cases of SSI: SSI effects (initial G and ξ), nonlinear SSI (corrected G and ξ) and stochastic SSI (random G with COV = 20%) compared to the fixed base case. Results show that the correction of G and ξ, according to the equivalent nonlinear method in all the cases, leads to a remarkable decrease in peak responses but show a huge amount of reduction in the second study for IBC-2015 and IS-1893-2002 codes compared to the other codes.