In order to evaluate the earthquake safety of equipment in structures, it is essential to analyze the In-Structure Response Spectrum (ISRS). The ISRS has a peak value at the frequency corresponding to the structural vibration mode, but the frequency and amplitude at the peak can vary because of many uncertain parameters. There are several seismic design criteria for ISRS peak-broadening for fixed base structures. However, there are no suggested criteria for constructing the design ISRS of seismically isolated structures. The ISRS of isolated structures may change due to the major uncertainty parameter of the isolator, which is the shear stiffness of the isolator and the several uncertainty parameters caused by the nonlinear behavior of isolators. This study evaluated the effects on the ISRS due to the initial stiffness of the bi-linear curve of isolators and the variation of effective stiffness by the input ground motion intensity and intense motion duration. Analyzing a simplified structural model for isolated base structure confirmed that the ISRS at the frequency of structural mode was amplified and shifted. It was found that the uncertainty of the initial stiffness of isolators significantly affects the shape of ISRS. The variation caused by the intensity and duration of input ground motions was also evaluated. These results suggested several considerations for generating ISRS for seismically isolated structures.