The red alga Gracilaria lemaneiformis was cultivated with the scallop Chlamys farreri in an integrated multi-trophic aquaculture (IMTA) system for 42 h at Sanggou Bay, located in north China. Variation in inorganic carbon in the IMTA system was determined. The experiment included three treatments each with three replicates and three scallop monoculture systems as controls. Scallop density (399.1 ± 7.85 g per microcosm) remained the same in all treatments while seaweed density differed. The seaweed density was set at three levels (treatments 1, 2, 3) with thallus wet weights of 125.3 ± 4.72 g, 252.3 ± 7.50 g, and 378.7 ± 6.51 g per microcosm, respectively. This produced bivalve to seaweed wet weight ratios of 1:0.31, 1:0.63, and 1:0.96 for treatments 1, 2, and 3, respectively. In control groups, continuous dissolution of carbon dioxide (CO2) produced by scallops into the seawater not only caused an ongoing increase in partial pressure of CO2 (pCO2), 5.5 times higher than that of natural seawater, but also acidified seawater by 0.8 units after 42 h of culture. However, in all seaweed-scallop groups, the higher the algal density, the more CO2 was absorbed; pCO2 was lowest in treatment 3. The results suggest that a ratio of bivalve to seaweed less than 1:0.96 may produce an even stronger CO2 sink. Overall, the integrated culture of seaweed and scallop could provide an efficient and environmentally friendly means to reduce CO2 emissions from bivalve mariculture.