Upper-ocean stratification acts as a physical barrier limiting the vertical mixing process and plays a crucial role in many biogeochemical processes of dissolved matter. This oceanographic phenomenon could be magnified due to global warming, influencing a wide range of dissolved matters’ marine fate and stock in the long term. Polycyclic aromatic hydrocarbons (PAHs), mainly from incomplete organic matter combustion or petrogenic sources, are of great concern because of their ubiquitous existence in the environment and their adverse health effects. By analyzing dissolved PAHs collected in global oceans and representative marginal seas, we found a common enrichment in the upper 300 m with the largest fluctuation in the surface mixed layer. The different ocean stratification degrees and primary productivity possibly give rise to the different patterns of PAH variations (ΔPAH) in the water column. Linear relationships (r2 = 0.52–0.58) were found between (Δ∑3-ringPAH)/(Δ∑4-ringPAH) and the stratification index for water-column PAHs, indicating that the contribution of three-ring PAHs increased with the stratification strengthened. A positive logarithm relationship (r2 = 0.50) was also found between the stratification index and ∑9PAH stock, suggesting the strengthened stratification could prompt PAH storage in the water column within a specific limit. As an amplified effect of global warming, the increased ocean stratification and their impact on organic pollutants should receive more attention.