<p indent="0mm">Carbon neutrality is an important concept in global climate change governance. Seagrass beds rank among the most productive autotrophic ecosystems on the planet, and are receiving increasing attention as globally-significant hotspots of organic carbon (“blue carbon”) sequestration. The blue carbon stored in seagrass beds has important implications for climate change mitigation. The protection of seagrass beds will also protect their organic carbon sequestration potential, consequently helping to achieve the goal of carbon neutrality. Unfortunately, about 29% of the world’s seagrass beds have been destroyed, with a loss rate of 7% a<sup>−1</sup> since 1990, mostly due to eutrophication. The organic carbon sequestration potential of seagrass beds could be influenced by the subsequent changes in organic carbon composition, and microbial transformation processes. We systematically reviewed the relevant local and international research to summarize the composition and microbial transformation of organic carbon and its responses to eutrophication. Organic carbon is present in various forms in seagrass beds, and can be roughly divided into primary producer living biomass carbon, litter organic carbon, water organic carbon, and sediment organic carbon according to its storage area. Organic carbon can also be divided into labile organic carbon (LOC), which is susceptible to microbial decomposition, and recalcitrant organic carbon (ROC), which is resistant to microbial decomposition. The total ROC (cellulose and lignin) content in seagrass is present in the range of <sc>153−561 mg/g,</sc> and accounts for more than 28.7% of the organic carbon in the seagrass plants. The ROC content of seagrass plants is affected by the species, morphology, tissue and organ types, and climatic zones. In the water column, color dissolved organic matter (CDOM) and neutral sugars are indicators of LOC, while the lignin phenol and humic-like fractions of fluorescent dissolved organic matter (FDOM) are potential tracers of ROC. The DOM in water can be divided into dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and dissolved organic phosphorus (DOP). The DOC/DON and DOC/DOP ratios are used to reflect DOC lability and microbial bioavailability, with high DON and DOP concentrations indicating high DOC lability. In sediments, extractable organic carbon and microbial biomass carbon are important indicators of LOC, while aromatic hydrocarbons and alkanes are indicative of recalcitrant components. There are significant differences in the sediment organic carbon contents of temperate and tropical regions. Microorganisms play a vital role in the transformation of organic carbon. There are geographic differences in microbial composition, which are mainly influenced by the available habitats and climate zones, but there are no differences between seagrass species within a fine-scale seagrass bed. Different microorganisms have different decomposition capacities. <italic>R</italic>-strategist microbes, including Clostridiales<italic> </italic>and<italic> </italic>Gammaproteobacteria, are able to rapidly decompose LOC, while <italic>k</italic>-strategists, such as Verrucomicrobiae<italic> </italic>and Anaerolinae, can break down the more recalcitrant compounds. There is a succession of <italic>r</italic>- to <italic>k</italic>-strategists microbes during the decomposition of fresh organic matter (including fresh seagrass litter, DOC, and SOC). Eutrophication may lead to the transformation of the community structure of primary producers in seagrass beds from seagrass to macroalgae, which will increase the input of labile carbon. This consequently causes an increase in LOC in the plant biomass, water column, and sediments, but a decrease in ROC. The nutrient loading can affect the microbial community structure and enzyme activity, which will affect the microbial transformation of organic carbon. Furthermore, nutrient and LOC inputs may induce a “priming effect” that promotes the remineralization of stored organic carbon. Several future research directions for determining the transformation of seagrass beds and their organic carbon were proposed. (1) Extensive studies of the organic carbon components (LOC and ROC) in seagrass beds are required. (2) There is a need to better understand the composition, function, and gene expression of microbial communities in seagrass beds. (3) The eutrophication mechanisms in microbial communities and the related extracellular enzyme activities need to be determined. (4) The response of the organic matter decomposition process to nutrient loading and the interaction of nutrients and algae need to be studied. There is also a need to strengthen local research on the carbon storage potential of seagrass beds to mitigate global climate change and provide theoretical support for achieving carbon neutrality.