The annual yield of shellfish aquaculture in China is reaching nearly 10 million tonnes. Carbon sequestration rate of the maricultured scallop Chlamys farreri in different areas of Sanggou Bay was measured in this study, and the main controlling factors in different areas were analyzed and discussed. Also, the comparability with terrestrial ecosystems was increased by standardizing carbon unit. No significant difference was found for scallop shell and soft tissue carbon content in different areas. However, differences in growth rate, stocking density and survival rate in different areas caused the differences in yield, which consequently resulted in different biological carbon sequestration rates in different areas. Carbon sequestration rate of cultured scallop C.farreri was comparable with the forest. In addition, shellfish farming activities had complicated the relationship with ecosystem carbon cycling in shallow water.Physiological processes such as feeding, breathing, bio-deposit and calcification need to be further studied in the future.