We propose a new method to estimate site amplification effects at specific sites, separating source and propagation-path effects. First, we calculate “specified spectra” from a given source and propagation-path effects, with a fixed site effect of 2.0. Then, we include effects of rupture process into the “specified spectra” using the empirical Green's function method. Site effects can be defined as a ratio of observed seismic spectra to the “specified spectra”. We applied this method to the ground motion data during the 1993 Kushiro-oki earthquake as strong motions and those of other small earthquakes as weak motions in the south-east area of Hokkaido. We found nonlinear site effects at the station KSR, in Kushiro city, where the maximum of horizontal amplitude was 711.4cm/s2 during the 1993 Kushiro-oki earthquake. The predominant frequency of the site effects became smaller and the amplification level of those at high frequencies became lower than those for the weak motions.