Recently, several countries have experienced strong earthquakes, and there has been growing interest in the seismic design of structures. Particularly, consideration of soil-structure interaction (SSI) has become important when performing seismic response analysis for nuclear power plant (NPP) structures. A seismic analysis method that considers SSI in the time domain has been proposed in previous studies. This method is applicable to the seismic response of structures, because it can consider the influence of the SSI effect with the impedance function in the frequency domain and simultaneously considers the structural nonlinearity. However, it has only been applied to the structure comprising a single beam-stick. In this study, a modified method for applying it to more general structures is proposed, and its applicability is validated with an actual reactor containment building (RCB) structure comprising a three beam-sticks. Validation was performed by comparing the seismic responses with those of ACS SASSI. Using the proposed method, SSI analysis was performed with three soil profiles and the results were compared to investigate the effect of SSI on seismic responses, including the in-structure response spectrum (ISRS) and time history acceleration. For more realistic analysis, soil profile and earthquake input motion occurred in South Korea are adopted. Further, a multi-step method considering nonlinear behavior was also performed and compared with the linear case.