Marine gas hydrates, one of the largest methane reservoirs on Earth, may greatly affect the deep sea sedimentary environment and biogeochemistry; however, the carbon geochemistry in gas hydrate-bearing sediments is poorly understood. In this study, we investigated the carbon variables in sediment core 973-3 from the southwestern Taiwan Basin in the South China Sea to understand the effect of environmental factors and archaeal communities on carbon geochemistry. The carbon profiles suggest the methanogenesis with the incerase of dissolved inorganic carbon (DIC) and high total organic carbon (TOC) (mean = 0.46%) originated from terrigenous organic matter (mean δ13CTOC value of ?23.6‰) driven by the abundant methanogen ‘Methanosaeta and Methanomicrobiales’. The active anaerobic oxidation of methane is characterized by the increase of DIC and inorganic carbon (IC), and the depleted δ13CIC, coupled with the increase of TOC and the decrease of δ13CTOC values owing to the methanotroph ‘Methanosarcinales/ANME’ in 430–840 cm. Environmental factors and archaeal communities in core 973-3 are significantly correlated to carbon variables owing to methane production and oxidation. Our results indicate that the carbon geochemical characteristics are obviously responding to the formation and decomposition of gas hydrates. Furthermore, pH, Eh and grain size, and Methanosaeta greatly affect the carbon geochemistry in gas hydrate-associated sediments.