This study investigated the influence of probabilistic variability in stiffness and nonlinearity of soil on response of nuclear power plant (NPP) structure subjected to seismic loads considering the soil-structure interaction (SSI). Both deterministic and probabilistic methods have been employed to evaluate the dynamic responses of the structure. For the deterministic method, SRPmin method given in USNRC SRP 3.7.2(2013) (envelope of responses using three shear modulus profiles of lower bound(), best estimate() and upper bound()) and SRPmax method (envelope of responses by more than three ground profiles within range of ) have been considered. The probabilistic method uses the Latin Hypercube Sampling (LHS) that can capture probabilistic feature of soil stiffness defined by the median and the standard deviation. These analysis results indicated that 1) number of samples shall be larger than 60 to apply the probabilistic approach in SSI analysis and 2) in-structure response spectra using equivalent linear soil profiles considering the nonlinear behavior of soil medium can be larger than those based on low-strain soil profiles.