To investigate the influence of the underlying sea surface layer on the buffeting response of long-span bridges, an offshore suspension bridge was selected as the subject. A numerical wave flume was constructed using the SST k-ω turbulence model and the Volume of Fluid (VOF) method. The evolution of wind profiles with the fetch distance over the water surface was analyzed. Addressing the issue of significant variations in aerodynamic forces on the girder with navigation clearance height due to the underlying surface layer, the “Effective Three-Component Force Coefficient Correction Method” was proposed. This method corrects the three-component force coefficients of the girder based on a gas-liquid two-phase flow model over a static water surface. Combining the harmonic synthesis method and time-domain buffeting analysis, the wind profile evolution, coefficient correction, and their coupled effects were quantitatively evaluated. Results indicate that: The wind profile evolution rate exhibits a trend of being “initially rapid followed by gradual”, stabilizing at a fetch distance of 1000 m. At this point, the buffeting response shows an average attenuation of 10% compared to the conventional uniform wind profile assumption. After correction, the deviation of the three-component force coefficients increases with decreasing height, leading to significant enhancement in lateral and torsional buffeting responses, with a maximum increase of 30%. Findings reveal that: Buffeting analysis for offshore bridges must fully account for the influence of the underlying surface layer, and the correction of the three-component force coefficients plays a particularly crucial role.