Abstract Hadal trenches are important reservoirs for the accumulation of organic carbon (OC) and dynamic hotspots for early diagenesis in the deep sea. This process is influenced by the sources of deposited organic material and the intense depositional dynamics driven by downslope forces and mass-wasting events. In this study, we examined water-extractable organic matter (WEOM), which represents free organic matter loosely associated with minerals, and base-extractable organic matter (BEOM), which denotes organic matter that is tightly bound to minerals, in eight sediment cores collected from four trenches: the Mariana, New Britain, Kermadec, and Atacama trenches. Utilizing ultrahigh-resolution mass spectrometry and optical spectrometry, we identified distinct molecular differences between WEOM and BEOM from the trench axis and adjacent non-hadal sites, respectively. BEOM was enriched in aromatic and humic molecules, whereas WEOM was characterized by a higher abundance of protein-rich molecules with presumed greater biolability. Although the concentration of WEOM was consistently lower than that of BEOM, the WEOM/BEOM ratio generally increased with sediment depth in both regions. Building on previous investigations of deposition dynamics in the Atacama Trench, our findings suggest a generalized hypothesis that variations in redox conditions within sediments contribute to the unique carbon cycling dynamics observed in hadal trenches. As sediment depth increases and iron minerals undergo gradual reduction, organic matter transitions from a mineral-bound state to a free state, subsequently migrating to surface sediments and overlying waters through diffusion. Given that the penetration depth of oxygen is significantly shallower in the trench axis, free organic matter migrates to the sediment-water interface over a shorter diffusion distance. This may result in a greater supply of labile substances to benthic microorganisms in the deepest regions of the ocean.