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Shellfish and algae mariculture make up an important part of the marine fishery carbon sink. Carbon sink research is necessary to ensure China achieves its goal of carbon neutrality. This study used the material quality assessment method to estimate the carbon sink capacity of shellfish and algae. Product value, carbon storage value, and oxygen release value were used to calculate the economic value of shellfish and algae carbon sequestration. The results showed that the annual average shellfish and algae carbon sink in China was 1.10 million tons from 2003 to 2019, of which shellfish accounted for 91.63%, wherein Crassostreagigas, Ruditapesphilippinarum, and Chlamysfarreri were the main contributors. The annual average economic value of China’s shellfish and algae carbon sequestration was USD 71,303.56 million, and the product value was the main contributor, accounting for 99.11%. The carbon sink conversion ratios of shellfish and algae were 8.37% and 5.20%, respectively, thus making shellfish the aquaculture species with the strongest carbon sink capacity and the greatest carbon sink potential. The estimated growth rate in the shellfish and algae removable carbon sink was 33,900 tons/year in China, but this trend was uncertain. The capacity for carbon sequestration and exchange by aquaculture can be improved by expanding breeding space, promoting multi-level comprehensive breeding modes, and marine artificial upwelling projects.