The spectral ratios of coda waves of local earthquakes have been often used as measures of relative amplification factors of different sites. Applying this method to coda waves registered by seismometers installed on the surface and at the bottom of a borehole, we succeeded in stably measuring the temporal change in site response associated with the occurrence of a large earthquake strong motion. A remarkable drop of coda spectral ratio and a shift of the peak frequency were observed during strong shake at two sites by the 2000 Western Tottori Earthquake and at a site by the 2003 Tokachi-Oki Earthquake in Japan. The reduction of the peak frequency reached 30--70% at all the sites. After that, the peak frequency logarithmically recovered to the value before the strong motions for a few years at two sites, whereas the other one quickly recovered in a few tens of minutes.