In the face of growing concerns over global climate change and carbon emissions, the study of marine carbon sinks has garnered significant attention. Shellfish aquaculture offers a promising pathway for carbon sequestration in marine ecosystems. Therefore, the determination of shell carbon content and the study of shell carbon degradation are critical approaches to understanding the carbon sink potential of shellfish farming. Filter-feeding shellfish not only achieve long-term carbon sequestration through shell calcification but also significantly impact the marine carbon cycle through their physiological activities and post-mortem degradation processes. Filter-feeding bivalves, as a crucial group in coastal aquaculture ecosystems, play a substantial role in carbon sequestration by filtering particulate organic carbon, such as phytoplankton and organic debris, during their growth processes. Additionally, they incorporate inorganic carbon into their shells, indirectly contributing to the enhancement of carbon sink functionality. The carbon content of bivalve shells in marine aquaculture accounts for 63.44%–92.64% of their total biomass carbon. The degradation of organic matter and the rate of organic carbon breakdown within the shells are also key factors determining the potential for long-term carbon sequestration in the shells. However, little is known about the carbon content in different bivalve species and various parts of their shells. Thus, precise measurements of shell carbon content and insights into the kinetics of organic carbon degradation are crucial for comprehending the carbon sequestration capacity of bivalves and evaluating the overall carbon sink potential of bivalve aquaculture. This study aims to accurately quantify the carbon content of shells and understand the degradation rates of shell carbon, providing fundamental data for deeper investigation into the role of shellfish in marine carbon sequestration. The following six species of filter-feeding bivalves were collected from Sanggou Bay in September 2022: Mytilus edulis, Chlamys farreri, Patinopecten yessoensis, Crassostrea gigas, Ruditapes philippinarum, and Scapharca subcrenata. An elemental analyzer was employed to measure the total carbon content and organic carbon content in different parts of the shells (edge, umbo, and entire shell). The total and organic carbon degradation rates were determined through indoor natural degradation experiments. The results indicated that the total and organic carbon contents varied among the different species. The total carbon content in the six species ranged from 11.31% to 13.37%, whereas the organic carbon content ranged from 0.53% to 2.17%. The total and organic carbon contents in M. edulis were significantly higher than those in the five other species (P<0.05), with no significant differences in total carbon content among the five remaining species (P>0.05). S. subcrenata exhibited significantly higher organic carbon content than the four other species, except for M. edulis (P<0.05). The total and organic carbon contents at the edge of M. edulis were significantly higher than those at the umbo (P<0.05), whereas the organic carbon content at the edge of S. subcrenata was also significantly higher than that at the umbo (P<0.05). No significant differences in total and organic carbon contents were found between the edge and the umbo in the four remaining species (P>0.05). The degradation rates of total and organic carbon in the shells varied by species, with higher organic carbon content leading to a faster total carbon degradation rate. The total carbon degradation rates (k445) of the six types of shells ranged from 0.021 9 a–1 to 0.080 3 a–1, with an average of (0.0511 ± 0.022 1) a–1. S. subcrenata had the highest total carbon degradation rate (k445 = 0.080 3 a–1), whereas R.phlippinarum had the lowest (k445 = 0.021 9 a–1). The degradation rates of S. subcrenata and M. edulis were significantly higher than those of the four other species (P<0.05). No significant differences in degradation rates were found among C. farreri, P. yessoensis, and C. gigas (P>0.05), whereas R.phlippinarum had a significantly lower degradation rate than the five other species (P<0.05). The organic carbon degradation rates (k445) ranged from 0.032 9 a–1 to 0.609 6 a–1. S. subcrenata had the highest organic carbon degradation rate (k445 = 0.609 6 a–1), whereas C. gigas had the lowest (k445 = 0.032 9 a–1). The degradation rate of S. subcrenata was significantly higher than those of the five other species (P<0.05), with no significant differences between C. farreri and R. phlippinarum (P>0.05) or among M. edulis, P. yessoensis, and C. gigas (P>0.05). Except for S. subcrenata, where the organic carbon degradation rate was significantly higher than the total carbon degradation rate (P<0.05), no significant differences were observed between total carbon and organic carbon degradation rates in the other species (P>0.05). In conclusion, R. philippinarum and C. gigas, as widely distributed representative species in coastal aquaculture systems, exhibit significant carbon sequestration potential. Therefore, further research and optimization of the cultivation models for these bivalves hold considerable theoretical and practical significance for enhancing marine carbon sequestration capacity and mitigating global climate change.