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This paper selected Sansha Bay which was a typical aquacultural bay in Fujian Province as the research area to investigate the current status of aquaculture, and calculated the amount and values of carbon sequestration contributed by mariculture from Sansha Bay. The results showed that the total aquaculture output of Sansha Bay in 2022 was 664 700 t, including 266 700 t of shellfish and algae. The dominant economic species included large yellow croaker, abalone, kelp, Gracilaria and oyster. The carbon ratio of these main cultured organisms varied spatially and temporally, ranging from 23.67% to 43.89% in tissues and 11.12% to 15.05% in shells. The carbon ratio of kelp decreased with the growth cycle, while the carbon ratio of shells showed no significant difference. In 2022, the mariculture of oysters, kelp, Gracilaria and other filter-feeding shellfish in Sansha Bay could remove carbon about 29 100 t from seawater, equivalent to reducing 106 700 t of CO2. It also created an economic value of 1.62 million yuan, with considerable carbon sequestration capacity and economic benefits. However, abalone, large yellow crock, sea cucumber and other bait-based culture organisms introduced about 925 500 t of extraneous carbon sources in the process of mariculture. Irrational input of bait and culture structure were important factors leading to the weak carbon sequestration ability of bait-based culture. This paper focused on the fishery carbon sink accounting of the typical aquaculture bay, and discussed the carbon sequestration capacity of locally bait-based aquaculture species. It would provide scientific basis for the aquaculture planning and the green upgrading and transformation of the aquaculture industry in this area.