The presence of sulfate-driven anaerobic oxidation of methane (SD-AOM) generally influences the precipitation of authigenic pyrite in seepage areas. However, the relatively weak comprehensive studies on the morphological and geochemical characteristics of pyrite limit the understanding of its formation and application to diagenetic processes. Here, we analyzed the pyrite texture, abundance, sulfur isotopic composition, degree of pyritization, and the trace element (TE) content of pyrite from two sites (A27 and SH1) in a seepage area of the South China Sea, so as to better constrain the impacts of SD-AOM on pyrite formation. Pore-water results revealed that present-day methane seepages occurred at both sites. Under normal sedimentary environments, pyrite resulting from organiclastic sulfate reduction (OSR) showed low abundances with negative δ34S. In contrast, high contents of 34S-enriched pyrite aggregates, long pyrite tubes and large framboid sizes typified by radial overgrowths were documented at the lower part of both core sediments, suggesting the significant impacts of SD-AOM. At the proposed sulfate-methane transition zone (SMTZ), pyrite is a mixing product of OSR and SD-AOM, but the latter enhances the morphologic and isotopic anomalies of pyrite. Besides, SD-AOM increased the degree of pyritization and accelerated the pyrite-iron accumulation in sediments. With pyritization proceeding, Mo, Ni, Mn, and Cr were gradually incorporated into the pyrite phase, presenting a relatively high affinity of these TEs for pyrite in the studied locations. However, the contents of TE in pyrite were positively correlated with its concentrations in the current ocean, from which we can get that TE in diagenetic pyrite was basically influenced by seawater chemistry. The comprehensive results reflect that the authigenic pyrite can act as an excellent geological archive of modern and ancient oceans. In particular, pyrite formed in seepage-impacted sediments allows identifying the methane seepage and characterizing the biogeochemical cycling of carbon, sulfur, and TEs.