Strong horizontal ground motions with the peak ground acceleration (PGA) larger than 1400 gal were observed at Yamamoto (MYGH10) station during the February 2021 Mj 7.3 off the east coast of Honshu, Japan, Fukushima earthquake. Firstly, in this paper, we discussed and verified the theoretical assumptions of the “Nakamura” method under weak and strong ground motions. The site amplification factor of the MYGH10 station was estimated using the surface horizontal-vertical spectral ratio (HVSR) and the surface-to-borehole spectral ratio (SBSR), and the corrected HVSRC, respectively. Meanwhile, the reasons for underestimating the site amplification factor when using HVSR were explained. The vertical amplification phenomenon of seismic P-wave in the high-frequency band was analysed under weak and strong ground motions. Secondly, we utilized HVSR, SBSR, and theoretical transfer function (TTF) based on the 1D wave propagation theory to study the nonlinear site response of MYGH10 station under the mainshock of the Fukushima earthquake and the historically weak and strong ground motions, respectively. The changes in frequencies and amplitudes of the spectral ratio curves when nonlinearities were occurring at the site were analysed and compared using the spectra ratio curves of weak ground motion records and TTF as references. Finally, the recovery of the site after strong nonlinearity was also evaluated by comparing the spectral ratio curves of aftershocks records. We found that the most significant amplification factor of the site increased from 7 to more than 10, and the predominant frequency decreased from 10 Hz to 3.8 Hz under the mainshock of the Fukushima earthquake. The predominant frequency returned to the previous value within three days after the mainshock, but the amplification factor did not.