Hydrodynamic processes control the transport of marine sediments in benthic environments of marginal seas, affecting the distribution of associated microbes and organic carbon (OC) composition in marine sediments. However, microbial characteristics variations and their impacts on OC composition during hydrodynamic transport processes remain poorly constrained. Here we analyzed the concentrations and carbon isotopes of phospholipid fatty acids (PLFAs), and conducted the thermal stability analysis on OC in grain sizes fractionated sediments retrieved along marine sediments transport pathway from the Yellow River delta to Yellow Sea. We find that the proportion of pre-aged and refractory OC compounds have correlations with relative abundance of anaerobic bacterial PLFAs, and bioavailable OC become more limited along the marine sediments transport pathway. We suggest that the conversion of different OC composition may facilitate the increasing abundance of anaerobic bacteria, and the metabolisms of microbes can utilize the refractory OC during resuspension of marine sediments. The metabolism of microbes attached to resuspension sediments may promote the pre-aged OC burial in marginal seas sediments, with important environmental implications such as carbon sequestration in benthic environment.