In this paper, firstly, acceleration-time histories were generated by varying strong motion duration in the frequency domain for application to a seismically isolated nuclear power structure, so as to examine the effects of strong motion duration on the behavior of the structure. Secondly, real recorded earthquakes were modified to match the target response spectrum based on the revised SRP 3.7.1(2007) and the modified time histories were applied to the analysis of a seismically isolated nuclear power structure. The obtained values of acceleration and displacement responses of the structure were, finally, compared with the values obtained in case of applying acceleration-time histories generated in the frequency domain to the structure.