The observed peak ground accelerations and peak ground velocities (PGVs) of the 2018 Mw 6.6 Hokkaido eastern Iburi earthquake generally followed the median values from ground motion prediction equations with reasonable errors at fault distances ≥ 50 km. However, at smaller distances, the equations significantly underestimated the peak ground motions, and it was eminent for PGVs. A comparison of surface-to-borehole spectral ratios of S-waves during the mainshock and other events revealed that the sites at smaller distances experienced various degrees of nonlinear site response. The two most widely known characteristics of nonlinear site response are the weakening of higher-frequency components and shifting of predominant frequencies to lower ones in comparison with the linear site response. At one of the sites that recorded the largest intensity of 7 in JMA scale of 0–7, the latter nonlinear effect was so dominant that the ground motions around the new predominant frequency got intensified by one order of magnitude in comparison with that during the weak-motions. Two sites, which were closely located, recorded vertical peak ground accelerations exceeding 1 g for the up-going motions. The recordings showed asymmetric waveforms and amplitudes characteristics of the nonlinear site response in extreme vertical ground motions recorded during a few earthquakes in the past. Few sites having lower vertical peak ground accelerations were also suspected of being experienced nonlinear site response on vertical motions. These findings suggest taking a cautious approach to enumerate the reduction in amplification at higher frequencies using the single-station horizontal-to-vertical (H-to-V) spectral ratio technique. However, we found that the H-to-V technique was still useful to detect nonlinearity. Finally, an ad hoc equation was derived to correct the nonlinear site amplification in predicting horizontal PGVs with respect to one of the most widely used attenuation models in Japan. The results indicated that the effect was much stronger for a larger input motion than that for a proportional change in the Vs30 values.