China is the largest mariculture country, and shellfish and algae output ranks first, showing high carbon sink capacity. In recent years, the single cultivation of macroalgae (Pyropia yezoensis) has been changed to macroalgae-shellfish mariculture in Haizhou Bay to increase the yield of P. yezoensis and improve the water environment quality. In this study, four surveys were carried out in July 2022 during the monoculture period of oyster (Magallana gigas), as well as at different stages of P. yezoensis culture (head-crop period, November 2022, peak growing season, January 2023, and end of harvesting, March 2023) in the mariculture and the surrounding waters of Haizhou Bay. The effects of different stages of culture on the seawater environment and seasonal and spatial variations in the carbonate system were analyzed, and the carbon sink capacity was preliminarily estimated. The results showed that in summer, the calcification of M. gigas and the primary production process of phytoplankton effectively reduced the dissolved inorganic carbon (DIC) level in the culture area. The culture area acts as a CO2 sink, with an average air-sea CO2 flux of −4.5 mmol m−2 d−1. During the polyculture period, the P. yezoensis culture activities maintained the stability of the seawater carbonate system, and the culture area shows strong CO2 sinks, with the average air-sea CO2 flux of −24.10 mmol m−2 d−1, -37.68 mmol m−2 d−1, and -38.99 mmol m−2 d−1, respectively. The absorption of CO2 by large-scale cultured P. yezoensis through the "biological pump" effect is the main factor affecting the CO2 exchange process at the air-sea interface, and the absorption rate of CO2 by P. yezoensis at the mature stage is higher than that at the growth stage before harvesting. The study revealed that macroalgae-shellfish mariculture could promote mutual growth, alleviate environmental pressure, and enhance the carbon sink of the culture area. The relationship between mariculture and the carbon cycle of a mariculture ecosystem is very complicated, and its biochemical process should be given great attention for further study.