Considering the non-linear behavior of structure and soil when evaluating a nuclear power plant's seismic safety under a beyond-design basis earthquake is essential. In order to obtain the nonlinear response of a nuclear power plant structure, a time-domain SSI analysis method that considers the nonlinearity of soil and structure and the nonlinear Soil-Structure Interaction (SSI) effect is necessary. The Boundary Reaction Method (BRM) is a time-domain SSI analysis method. The BRM can be applied effectively with a Perfectly Matched Layer (PML), which is an effective energy absorbing boundary condition. The BRM has a characteristic that the magnitude of the response in far-field soil increases as the boundary interface of the effective seismic load moves outward. In addition, the PML has poor absorption performance of low-frequency waves. For this reason, the accuracy of the low-frequency response may be degraded when analyzing the combination of the BRM and the PML. In this study, the accuracy of the analysis response was improved by adjusting the PML input parameters to improve this problem. The accuracy of the response was evaluated by using the analysis response using KIESSI-3D, a frequency domain SSI analysis program, as a reference solution. As a result of the analysis applying the optimal PML parameter, the average error rate of the acceleration response spectrum for 9 degrees of freedom of the structure was 3.40%, which was highly similar to the reference result. In addition, time-domain nonlinear SSI analysis was performed with the soil's nonlinearity to show this study's applicability. As a result of nonlinear SSI analysis, plastic deformation was concentrated in the soil around the foundation. The analysis results found that the analysis method combining BRM and PML can be effectively applied to the seismic response analysis of nuclear power plant structures.