In order to improve the seismic performance of structures, friction pendulum system (FPS) is the most commonly used seismic isolation device in addition to lead rubber bearing (LRB) in high seismicity area. In a nuclear power plant (NPP) with a large self weight, it is necessary to install a large number of seismic isolation devices, and the position of the center of rigidity varies depending on the arrangement of the seismic isolation devices. Due to the increase in the eccentricity, which is the difference between the center of gravity of the nuclear structure and the center of stiffness of the seismic isolators, an excessive seismic response may occur which could not be considered at the design stage. Three different types of eccentricity models (CASE 1, CASE 2, and CASE 3) were used for seismic response evaluation of seismically isolated NPP due to the increase of eccentricity (0%, 5%, 10%, 15%). The analytical model of the seismic isolation system was compared using the equivalent linear model and the bilinear model. From the results of the seismic response of the seismically isolated NPP with increasing eccentricity, it can be observed that the effect of eccentricity on the seismic response for the equivalent linear model is larger than that for the bilinear model.