In 2016, a countermeasure against the Nankai trough long-period and long-duration ground motions (LPGMs) was announced. However, the response spectrum method (RSM), indicated by the Ministry of Construction notification Vol. 2009, is out of countermeasure. In the case of using RSM for the example waveform of LPGMs published in countermeasure, it tends to overestimate the velocity response of the seismic isolation interface. In this paper, we proposed the method of evaluating velocity response of the seismic isolation interface based on the periodic characteristics of the design response spectra for LPGMs.