This paper aims to evaluate the applicability of the equivalent linear analysis method for reinforced concrete, which uses frequency-independent hysteretic damping with a small computational load, to the seismic design of reactor building of the nuclear power plant. To achieve this, we performed three-dimensional FEM analyses of the soil-structure interaction system, focusing on the nonlinear and equivalent linear seismic behavior of a reactor building under an ideal soil condition. From these results, the method of equivalent analysis showed generally good correspondence with the method of the nonlinear analysis, confirming the effectiveness. Moreover, the method tended to lower the structural stiffness compared to the nonlinear analysis model. Therefore, in the evaluation of the maximum shear strain, we consider that the results were more likely to be higher than the results of nonlinear analysis.