The shellfish and algae carbon sinks as an important part of the fishery carbon sinks. It is of great significance to evaluate the current development status of shellfish and algae carbon sinks for the development of fishery carbon sinks and realization of carbon neutrality. There are a lot of studies on the quantitative relationship of shellfish and algae carbon sinks, but few researches on its spatial relationship. This study used the Natural Breaks and Standard Deviation Ellipse (SDE) in Geographic Information System (GIS) to analyze the spatial evolutionary characteristics of China’s shellfish and algae carbon sinks from 1992 to 2021. The results show that spatial distribution of carbon sinks varied widely in different regions, the overall spatial layout was stable and gradually formed a pattern of integrated and coordinated development of key regions and general regions. The structure of the shellfish and algae carbon sinks was unbalanced in China, in which algae carbon sinks had great potential for development. China’s shellfish and algae carbon sinks had strong resilience after natural disasters. Based on the above findings, this study suggests that all regions should increase the total output of shellfish and algae, expand the scale of algae, and achieve a balanced development of the shellfish and algae industry. Local governments should introduce marine environmental governance policies according to local conditions to achieve precise intervention in key carbon sink areas and overall governance in general carbon sink areas. The government should actively promote the expansion of shellfish and algae mariculture scale. This study will provide reference for the future development of China's fishery carbon sinks.