The 2018 Hokkaido Iburi-Tobu earthquake occurred on September 6. In this earthquake, seismic intensity 7 was measured at Shikanuma, Atsuma Town, and severe damage occurred in Hokkaido. The strong motions were recorded at observation stations including those nearby the epicenter, and the seismograms at a few stations close to the epicenter showed pulse-like waveforms. In the region called Yufutsu Plain, the underground structure is quite complex because Yufutsu Plain is located at the western margin of the Hidaka collision zone. Thus, the mechanism of generating the observed high-amplitude ground motions in this area has not been clarified yet. We performed the generalized inversion technique to estimate the fundamental characteristics of source terms and site amplifications at Yufutsu area to investigate the mechanism mentioned above. We found that the stress drop of the mainshock of the 2018 Hokkaido Iburi-Tobu earthquake was approximately 10Mpa, which corresponds to the upper limit of the crustal earthquakes in the past, and that the short-period level A was approximately 1.17x10(19) N<bold>m</bold>. We also evaluated the site amplification at sites close to the aftershock zone. We found that the sites in the north with relatively high altitudes showed dominant frequencies above several Hz, while the sites in the south with relatively low altitudes showed dominant frequencies of approximately 1Hz or lower. We also found that the site amplifications were quite large at three sites (BBC, HKD126 and IBUH03) where we observed clear pulse-like waveforms, and confirmed that they all showed dominant frequencies at approximately 1Hz.