This study analyzes 6 436 offshore ground motion records from 496 seismic events observed by seafloor observation network for earthquakes and tsunamis along the Japan Trench (S-net), aiming to investigate the frequency content characteristics of vertical ground motion components. Using random-effects regression with consideration of key factors like water depth and sediment layer thickness, we developed empirical models for vertical frequency content parameters. Significance tests and the Akaike Information Criterion (AIC) were employed to evaluate parameter validity and model goodness-of-fit. Results show that significant differences exist between horizontal and vertical frequency content distributions, highlighting the significance of the water depth parameter and setting condition. For S-net ocean-bottom stations (water depth: 102~7830 m), vertical frequency parameters shift toward shorter periods at depths less than 1500 m, while longer-period (longer than 0.8 s) records increase significantly at depths greater than 1 500 m. The water depth significantly affects vertical frequency content. Predictions for different tectonic types show consistent differences between vertical and horizontal models. Site terms exhibit significant differences between inner-trench and outer-trench stations, possibly influenced by the propagation paths of seismic waves and the topographical features associated with the outer ridge of the trench rather than sediment layer thickness. This study provides support for understanding offshore ground motion characteristics and assessing offshore seismic hazards.