Marine sediments constitute the most extensive carbon reservoir and sink on Earth, playing a pivotal role in regulating global climate dynamics. In recent years, with the growing influence of mariculture on the marine carbon cycle, it has become imperative to examine the effects of mariculture activities on sedimentary carbon content. This study was conducted from May 2023 to January 2024 in the mussel suspended mariculture area of Gouqi Island in Zhejiang Province, focusing on the impact of large-scale mussel farming activities on the temporal and spatial variation characteristics of sediment carbon fractions. It further examined the primary environmental determinants influencing sediment carbon content and assessed the contribution of mussel aquaculture to sediment organic carbon sources through the analysis of stable carbon and nitrogen isotopes. The results revealed substantial spatial heterogeneity in the distribution of sediment carbon content between the cultivation zone and control area. Notably, the total carbon and inorganic carbon content were significantly higher in the cultivation zone compared to the control area. However, no significant difference was detected in organic carbon content. Boruta models indicated that the total sediment carbon within the cultivation area was primarily influenced by pH levels and silicate content, with importance values of 5.88 and 5.17, respectively. The distribution characteristics of sediment organic carbon content were chiefly determined by total nitrogen and pH. In contrast, the C/N ratio and chlorophyll concentrations significantly affected the inorganic carbon content in sediments, with importance values of 10.72 and 7.97, respectively. Furthermore, the results from the MixSIAR stable isotope mixing model demonstrated that terrestrial sources were the principal contributors to the organic carbon in cultured mussel sediments. The biological deposition by mussels constituted 22.21%±3.08% of the organic carbon sources in the sediments, a proportion significantly greater than that observed in the control area. Regarding sediment carbon storage, the culture area was primarily composed of non-decomposable and underutilized inorganic carbon components, thereby enhancing the stability of the sediment carbon pool. In contrast, the sediment composition in the control area was dominated by humified organic matter, which impeded the efficient storage of carbon within the pool. This study highlights the significance of both shellfish biodeposition and inorganic carbon components as essential factors in the assessment of sediment carbon pools within mariculture environments. The research findings offer a critical scientific basis for further investigation into the impact of shellfish raft culture on sediment carbon cycle processes and its contribution to carbon sequestration mechanisms.