In the dynamic soil-structure interaction(SSI) analysis, numerous uncertain parameters are involved. They include the uncertainties in the definition of input motions, modeling of soil-structure interaction systems. analysis techniques, etc. This paper presents the results of parametric studies of the seismic responses of a reactor containment structure built on the viscoelastic layered soil. Among the numerous parameter, this study concentrates on the effects of definition point of the input motion, embedment of structure to the base soil, thickness of the top soil layer, and rigidity of the base soil. The substructure method using frequency independent impedances is adopted. The method is based on the mode superposition method in time domain using the composite modal damping values of th SSI system computed from the ratio of dissipated energy to the strain energy for each model. From the study results, the sensitivity of each parameter on the earthquake responses has been suggested for the practical application of the substructure method of SSI analysis.