While marine dissolved organic matter (DOM) represents one of the largest reservoirs of reduced carbon on the surface of the earth, its characterization, distribution pattern and associated biogeochemical processes in marine sediments have yet to be full studied, especially in deep layers. In this study, we investigated porewater DOM in sediments over glacial-interglacial cycles in the northern South China Sea. Fluorescence excitation-emission matrices were used to characterize fluorescent DOM (FDOM) and three FDOM components were identified for porewater DOM. The intensity of all FDOM components increased with increasing depth from the surface layer, suggesting that FDOM accumulated with time. Along the period from Marine Isotope Stage (MIS) 3 to MIS 1, the molecular weight (MW) of FDOM kept quite stable, although FDOM in MIS 3 has been degraded for a longer time and was supposed to have a lower MW. This may attribute to higher MW labile DOM produced in MIS 3 resulting from higher primary productivity and stronger mixing effect compared to MIS 1. Based on fluorescence index and δ¹³C value, FDOM in this study was mainly marine autochthonous (algae, microbial-derived). Thus, we further explored the potential role of sedimentary bacterial communities in regulating the distribution pattern of FDOM. Bacterial functions associated to thorough degradation of DOM were found to be more abundant in MIS 1, which may contribute to reduce the molecular weight of DOM in this period. The beta-diversity and co-occurrence networks of the bacterial community also gave some hints to explain the distribution pattern of FDOM.