Given the significant influence of wave propagation on the airflow structures and aerodynamic behavior of sea-crossing bridge decks, understanding the effects of the dynamic wave boundary layer (WBL) on vortex-induced vibration (VIV) is crucial. This study proposes a numerical simulation framework to investigate how dynamic WBL impacts VIV characteristics of sea-crossing bridge decks. A wave-following mesh scheme with periodic boundary conditions generates homogeneous dynamic WBL airflows. These validated flow conditions are integrated into a two-dimensional unsteady Reynolds-averaged Navier–Stokes (URANS) simulation incorporating fluid–structure interaction to analyze the VIV response of a sea-crossing bridge deck. Simulation results reveal that the oscillatory wind field induced by waves alters vortex shedding and deck surface pressure distribution, thereby disrupting VIV onset conditions and reducing its amplitude. Specifically, as the deck approaches the wave surface, the influence of waves on the aerodynamic performance of the deck becomes more pronounced, leading to a reduction in VIV amplitude with decreasing deck-wave clearance. Notably, under wind speeds outside the VIV range, dynamic WBL induces forced deck vibrations. In such cases, deck vibration frequency and phase synchronize with wave motion, and reduced deck-wave clearance amplifies forced vibration amplitude.