As an important part of groundwater systems, aquitards may have a considerable impact on the quality of groundwater in an aquifer. Organic carbon (OC) serves as an important component in biogeochemical processes which affects the hydrochemical composition of pore water; the association of OC with (Iron) Fe-containing minerals is recognized as an important stabilization mechanism for OC. However, the characteristics of the process forming complexes between OC and Fe oxides in subsurface aquitards and the contribution of OC to aquifers has been poorly understood. In this study, the content, speciation and reaction types of OC and Fe oxides were investigated to reveal the characteristics and mechanisms of OC-Fe interaction in subsurface aquitards at different depths in two typical sedimentary facies of the Jianghan Plain in central China. The total organic carbon (TOC) contents of aquitard sediments in alluvial-lacustrine and residual slope facies were 7.25 ± 5.10 and 2.79 ± 0.86 mg g−1, respectively. In general, the proportion of the heavy fraction of OC (HFOC) to TOC gradually increased with increasing depth because consumption of the light fraction of OC (LFOC) that caused more HFOC to remain in sediment. On average, Fe bound-OC contributed 30.3% and 31.6% of TOC by adsorption and coprecipitation, respectively. The adsorption-stabilized OC has not changed obviously but the coprecipitation-stabilized OC increased gradually with depth. Coprecipitation stabilized more OC in a stable environment (residual slope facies) when compared with an unstable environment (alluvial-lacustrine facies), which can be supported by the greater average ratio of FePP bound-OC:TOC ratio and increased enrichment of carboxylates and aromatics in a stable environment. The transformation of OC-Fe complexes could affect the transport of As, Cr and ammonium which chemically bind to organic matter (OM) and Fe minerals from sediment to pore water by reductive dissolution. The findings of this study are helpful in understanding the interaction between OC and Fe oxides in subsurface aquitard environments, in which reaction products may affect adjacent aquifers.