Marine sediment is one of the Earth’s largest organic carbon sinks. Microbial transformation of carbon is considered a key process influencing the carbon flow in sediment and ultimately atmospheric oxygen and carbon dioxide concentrations. Nevertheless, the controls on microbial organic carbon cycling are not well understood, including the biogeochemical role of Archaea, which are often abundant in marine sediments. We conducted a series of studies on the roles of microbes in organic matter transformation in the sediments of South China Sea, particularly focusing on recalcitrant carbon degradation and methane transformation. In correspondence to microbial carbon pump in marine sea water, we propose a schematic model S-MCT to guide our understanding and further studies on microbial roles in carbon remineralization and sequestration in marine sediments.