The sinks/sources of carbon in the Yellow Sea (YS) and East China Sea (ECS), which are important continental shelf seas in China, could exert a great influence on coastal ecosystem dynamics and the regional climate change process. The CO2 exchange process across the seawater-air interface, dissolved and particulate carbon in seawater, and carbon burial in sediments were studied to understand the sinks/sources of carbon in the continental shelf seas of China. The YS and the ECS generally have different patterns of seasonal air-sea CO2 exchange. In the YS, regions west of 124°E can absorb CO2 from the atmosphere during spring and winter, and release CO2 to the atmosphere during summer and autumn. The entire YS is considered as a CO2 source throughout the year with respect to the atmosphere, but there are still uncertainties regarding the exact air-sea CO2 exchange flux. Surface temperature and phytoplankton production were the key controlling factors of the air-sea CO2 exchange flux in the offshore region and nearshore region of the YS, respectively. The ECS can absorb CO2 during spring, summer, and winter and release CO2 to the atmosphere during autumn. The annual average exchange rate in the ECS was −4.2±3.2 mmol m−2 d−1 and it served as an obvious sink for atmospheric CO2 with an air-sea exchange flux of 13.7×106 t. The controlling factors of the air-sea CO2 exchange in the ECS varied significantly seasonally. Storage of dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) in the YS and the ECS were 425×106 t and 1364×106 t, and 28.2×106 t and 54.1×106 t, respectively. Long-term observation showed that the DOC content in the YS had a decreasing trend, indicating that the “practical carbon sink” in the YS was decreasing. The total amount of particulate organic carbon (POC) stored in the YS and ECS was 10.6×106 t, which was comparable to the air-sea CO2 flux in these two continental shelf seas. The amounts of carbon sequestered by phytoplankton in the YS and the ECS were 60.42×106 t and 153.41×106 t, respectively. Artificial breeding of macroalgae could effectively enhance blue carbon sequestration, which could fix 0.36×106–0.45×106 t of carbon annually. Organic carbon (OC) buried in the sediments of the YS was estimated to be 4.75×106 t, and OC of marine origin was 3.03×106 t, accounting for 5.0% of the TOC fixed by phytoplankton primary production. In the ECS, the corresponding depositional flux of OC in the sediment was estimated to be 7.4×106 t yr−1 , and the marine-origin OC was 5.5×106 t, accounting for 5.4% of the phytoplankton primary production. Due to the relatively high average depositional flux of OC in the sediment, the YS and ECS have considerable potential to store a vast amount of “blue carbon.”