In order to increase the seismic safety of nuclear power plant (NPP) structures, a technique to reduce the seismic load transmitted to the NPP structure by using a seismic isolation device such as a lead-rubber bearing has recently been actively researched. In seismic design of NPP structures, three directional (two horizontal and one vertical directions) artificial synthetic earthquakes (G0 group) corresponding to the standard design spectrum are generally used. In this study, seismic analysis was performed by using three directional artificial synthetic earthquakes (M0 group) corresponding to the maximum-minimum spectrum reflecting uncertainty of incident direction of earthquake load. The design basis earthquake (DBE) and the beyond design basis earthquakes (BDBEs are equal to 150%, 167%, and 200% DBE) of G0 and M0 earthquake groups were respectively generated for 30 sets and used for the seismic analysis. The purpose of this study is to compare seismic responses and seismic fragility curves of seismically isolated NPP structures subjected to DBE and BDBE. From the seismic fragility curves, the probability of failure of the seismic isolation system when the peak ground acceleration (PGA) is 0.5 g is about 5% for the M0 earthquake group and about 3% for the G0 earthquake group.