The function of carbon sinks in marine aquaculture have been gradually recognized and affirmed; therefore, marine aquaculture is no longer merely an economic activity, but a positive carbon ecological activity. This research focused on fishery carbon sinks as a main process for transferring carbon from aquatic products during harvest. According to the data of marine aquaculture production in the coastal areas of the China Fishery Yearbook, we studied 9 coastal provinces of China and selected the major species of shellfish and algae for this study. Dry and wet weight carbon coefficients of the selected marine products were obtained from reported values in the literature; then we combined those values with the yield data to obtain the mariculture carbon sinks of different biological species in the coastal provinces of China. Since there is a relationship among carbon sinks, a carbon sink coefficient and the yield of different species, we measured the annual carbon sequestration capacity of aquaculture seawater in the coastal areas of China from 2008 to 2015. Furthermore, we divided the coastal provinces into different sea areas to compare the carbon sink capacity and carbon sink conversion ratio of the Bohai Sea, the Yellow Sea, the East China Sea, and the South China Sea. Finally, from the perspective of the structural effects and scale effects of marine aquaculture carbon sinks, we identified the main factors that affect the carbon sink potential of coastal areas in China using an LMDI model. The potential for carbon sinks in the different sea areas were comprehensively evaluated. The results showed that since 2008 the amount of carbon in China's marine aquaculture industry has exceeded 1.05 million tons. The carbon sink conversion ratio and carbon sink capacity of coastal provinces has increased over the years, indicating that the carbon sink capacity of China's marine aquaculture industry cannot be neglected. Shellfish can significantly increase the carbon sink conversion ratio; therefore, the carbon sink conversion ratio of the South China Sea was the highest and had the best culture structure of the 4 sea areas, and that of the East China Sea was the lowest. The conversion ratio of carbon sinks along the Bohai Sea and the Yellow Sea coast were similar. From the time dimension, the carbon sink conversion ratio in the South China Sea was stable, while the East China Sea had a significant downward trend of carbon sink conversion ratio due to its aquaculture structure, which is biased towards algae. The carbon sink capacity of each sea area has increased over time, with the highest in the Yellow Sea and the lowest in the Bohai Sea before 2012 and the lowest in the South China Sea after 2012. The gap among the different sea areas has increased each year. An LMDI method compared the effects of aquaculture structure and the scale effect on the carbon sink capacity of China's marine aquaculture industry. It was found that the scale effects of each sea area were always positive, while the structural effect were sometimes significantly negative. In some years, the changes in aquaculture structure inhibited the carbon sinks, indicating that the structural effects were more significant but unstable. Based on the above conclusions, China's coastal carbon sequestration industry should improve carbon sink technology and stabilize marine aquaculture production, followed by optimizing the aquaculture structure and paying more attention to shellfish with large carbon sink potential.