Structures in a nuclear power system are designed to be elastic even under an earthquake excitation. However a structural component such as an isolator shows inelastic behavior inherently. For the seismic assessment of nonlinear structures, response history analysis should be performed. In this study, the response of base isolation system was analyzed by response history analysis for the seismic performance assessment. Firstly, several seismic assessment criteria for a nuclear power plant structure were reviewed for the nonlinear response history analysis. Based on these criteria, the spectrum matched ground motion generation method modifying a seed earthquake ground motion time history was adjusted. Using these spectrum matched accelerograms, the distribution of displacement responses of the simplified base isolation system was evaluated. The resulting seismic responses excited by the modified ground motion time histories and the synthesized time history generated by stochastic approach were compared. And the response analysis of the base isolation system considering the different intensities in each orthogonal direction was performed.