According to natural frequency of soil, characteristics of earthquake responses of an isolated containment building in nuclear power plants are examined. For this, earthquake response analysis of seismically isolated containment buildings in nuclear power plants is carried out by strictly considering soil-structure interactions. The structure and near-field soil are modeled by the finite element method while far-field soil by consistent transmitting boundary. The equation of motion of a soil-structure interaction system under incident seismic wave is derived. The derived equations of motion are solved to carry out earthquake analysis of a seismically isolated soil-structure system. Generally, the results of this analysis show that seismic isolation significantly reduces the responses of the soil-structure system. However, if the natural frequency of the soil is similar to that of the soil-structure system, the responses of the containment buildings in nuclear power plants rather increases due to interactions in the system.