Abstract: Ensuring the safety of coastal and offshore projects subjected to strong earthquakes is a major engineering challenge. A two-dimensional nonuniform gridding and fine finite element model for the seabed cross-section site in Jintang Strait is established using the geological and geotechnical exploration data. According to the regional tectonic setting and historical seismicity around the undersea tunnel site, the downhole array bedrock records during two strong earthquakes are selected as the input bedrock motions, the spatial inhomogeneous variation, nonlinear and hysteretic behaviors of the seabed soil are considered, and the site responses of the seabed deep deposits under various earthquake levels are simulated using the parallel method. The significant amplification and filtering effects of seismic propagation for the low-frequency components below 1 Hz and the high-frequency components higher than 10 Hz of the bedrock motions are observed in the site responses. With the increase of bedrock motion levels, the values of acceleration transfer function of the seabed site decrease, and the predominant frequencies of the seabed site response tend to be lower. The peak acceleration amplification factors of the seabed surface are obviously lower than those of the general land sites. The 5% damping spectral acceleration spectra and the cumulative absolute velocity at the seabed surface are significantly affected by the bedrock motion characteristics and seabed local site conditions. The coupled horizontal and vertical bedrock motions exhibit a substantial negative influence on the design ground motion parameters of the seabed site, compared to those in the cases of only the horizontal bedrock shaking. The determination of the design ground motion parameters of the seabed site based on the current seismic code may be unsafe.