In this paper, the seismic analysis model for seismically isolated KALIMER reactor structures is developed and the modal analysis and the seismic time history analysis are carried out for seismic isolation and non-isolation cases. To check the seismic stress limit according to the ASME Code, the equivalent seismic stress analyses are preformed using the 3-D finite element model. From the seismic stress analysis, the seismic margins are calculated for structural members. The limit of seismic load is defined to show that the maximum input acceleration ensures the structural safety for seismic load. In comparison of seismic responses between seismic isolation and non-isolation cases, the seismic isolation design gives significantly reduced acceleration responses and relative displacements between structures. The seismic margin of KALIMER reactor structure is high enough to produce the limit seismic load 0.8g.