Observation of aftershocks of the 2003 Tokachi-Oki earthquake was conducted in the southern part of the Tokachi basin in Hokkaido, Japan for estimation of local site effects. We installed accelerographs at 12 sites in Chokubetsu, Toyokoro, and Taiki areas, where large strong motion records were obtained during the main shock at stations of the K-NET and KiK-net. The stations of the aftershock observation are situated with different geological conditions and some of the sites were installed on Pleistocene layers as reference sites. The site amplifications are investigated using spectral ratio of S-waves from the aftershocks. The S-wave amplification factor is dominant at a period of about 1 second at the site near the KiK-net site in Toyokoro. This amplification fits well with calculated 1D amplification of S-wave in alluvial layers with a thickness of 50 meters. In addition to the site effects, we detected nonlinear amplification of the soft soils only during the main shock. The site effects at the strong motion site of the K-NET at Chokubetsu have a dominate peak at a period of 0.4 seconds. This amplification is due to soft soils having a thickness of about 13 meters. Contrary to the results at the two areas, site effects are not significantly different at the stations in the Taiki area, because of similarity on surface geological conditions.