China is the largest mariculture country of shellfish and seaweed in the world. The total annual yields of these in 2002 are more than 10 million tons. Among of which, the yields of seaweed and shellfish are 1.3 and 9.7 million tons, respectively. Seaweeds can transform dissolved inorganic carbon into organic carbon by photosynthesis; filtering shellfish can clear out particle organic carbon by feeding activity and through the process of calcification a lot of carbon can be imbedded into the shells at the form of CaCO3. Especially, a mass of carbons can be removed out of ocean through harvest, which must have great influence on the carbon cycle of coastal ecosystem. Through the activity of shellfish and seaweed mariculture, there were more than 3 million tons carbon being utilized and about 1.2 million tons carbon being taken away from the shallow sea by harvesting, which is calcultated basing on the data of annual production, the C content of both shellfish and seaweed and the energy budget of shellfish. Most important was that there were about 670000 tons carbon were fixed by shells and became the long-term carbon sink. The result not only discusses a new clue for probing into the question of “missing sink” in the global carbon cycle, but also testifies that the aquaculture of shellfish and seaweed in the coastal ocean can utilize a great deal of oceanic carbon directly or indirectly and improve the capacity of shallow sea absorbing atmospheric CO2. In addition, the relationship between the aquaculture and the carbon cycle of the coastal ecosystem is very complicated and its interaction is evident, consequently, its biogeochemical process should be paid great attention for further and deeply study as a science problem.