Microbially-mediated methane, S and Fe cycling in the sediments can largely reduce the flux of methane from the ocean to the atmosphere. Compared to a large number of records regarding these processes in the sulfate-methane transition zone (SMTZ), detailed information of these processes in the zone above the SMTZ is still required. In this study, a short sediment core DS16 (330 cm) collected from the methane hydrate-bearing Dongsha area, Northern of the South China Sea, was examined by geochemical and microbial methods. Pore water dissolved inorganic carbon (DIC) had an increasing trend with the increasing depth of the sediment, while the value of delta C-13-DIC showed a decreasing pattern. The high concentrations of DIC (up to 32.88 mM) and relatively negative delta C-13-DIC (down to -30.07%0) indicated the occurrence of anaerobic oxidation of methane (ACM) to some extant above the SMTZ in this region. The variation of concentration profiles of H2S (3.69-12.71 mmol/L) and Fe(III) indicated active S and Fe redox reactions occurred in this zone. Notably, both of the decreasing trends of sulfate and Fe(M) correlated well with those of delta C-13-DIC, indicating AOM and organic materials coupled with both sulfate and Fe(III) reduction. Moreover, high-throughput sequencing data showed that a number of archaea (ANME-1) and bacteria (Sulfurovurn and Shewanella), which are potential methane-, S-and Fe-metabolic related microorganisms, were detected in these sediments. In addition, the functional genes related to sulfate reduction, sulfur oxidation, and Fe uptake were also detected based on metagenomics analysis. Among them, with the depth increase and Fe(III) concentration decrease, the gene related to Fe3+ uptake mechanism decreased, while the gene related to siderophore uptake mechanism remained constant or even slightly increased. Thus, we propose that bacteria acquired Fe(III) via Fe(III) uptake proteins and siderophore uptake proteins in the Fe-deficient environments for reduction, which then might support the occurrence of Fe-ACM. By integrating these data, we suggest the occurrence of active biogeochemical CH4-S-Fe cycling in the zone above the SMTZ under high methane flux.