<p>Wave-induced vertical movement of the survey vehicle during Sub-Bottom Profiler (SBP) surveys can cause swell noise, regular offsets of travel time of the seafloor. This noise significantly reduces the signal-to-noise ratio and resolution of the profile. It is crucial to eliminate the influence of swell noise in order to improve the quality of sub-bottom profiles. However, how to accurately eliminate swell noise and handle large volumes of sub-bottom profile data is a challenging job. In this paper, we propose a novel swell static correction method for SBP data based on Variational Mode Decomposition (VMD) that is capable of automatic processing. The method require neither external information or manual intervention during the correction process, making it well-suited for large-scale SBP data processing. The only parameter required is the number of decomposition modes <i>k</i>,;in most cases, we found <i>k</i> = 5 to be appropriate. Model tests suggest that the method is highly effective when the wavelength of the wave-induced seafloor oscillation is less than one-tenth of the wavelength of the true seafloor undulation. Field data results demonstrate that our VMD-based method outperforms the conventional filtering approaches—low-pass, moving-average/median, and Gaussian—commonly used for swell static correction of seafloor picks in SBP/shallow sub-bottom profiling and widely reported as operational baselines, particularly for SBP data collected in slope environments.</p>