With the increasing pressure of resource decline and environmental pollution faced by the green transformation of marine fisheries, marine fishery carbon sinks are an increasingly close link to national strategic interests and economic lifelines. It is, therefore, necessary to explore paths for the enhancement and development of the carbon sink capacity of marine fisheries. Based on the economic data of marine fisheries from 2002 to 2021, this paper measures the capacity and characteristics of marine fishery carbon sinks in provincial areas, applies the kernel density estimation method to depict the dynamic evolution of the distribution of absolute differences in marine fishery carbon sinks, and at the same time, identifies the factors influencing the spatial imbalance in the development of marine fishery carbon sinks as well as the spatial spillover effects. The results show the following: (1) From the total amount, the fishery carbon sink capacity of China’s three marine economic circles has fluctuated and increased over the past 20 years, with obvious differences among different circles, and the marine fishery carbon sink capacity of the eastern, northern, and southern marine economic circles has risen sequentially. This trend corresponds to the economic disparities among the three circles, demonstrating a transition from economic to industrial driving effects. (2) From the spatial point of view, the fishery carbon sink capacity shows a trend of increasing year by year, concentrating in the circles, and overflowing between the circles. (3) The results of a partial derivative test further show that among the main influencing factors of marine fishery carbon sinks, capital, labor, and market openness have direct positive effects on marine fishery carbon sinks, and the direct effect of innovation is the strongest, and the significance of the indirect effect of the three circles is weaker compared to the direct effect and total effect. As a result, the carbon sink of China’s marine fisheries has a large room for improvement, and in order to promote the high-quality development of China’s marine fisheries, it is still necessary to accelerate the circulation of resources within the marine economic circle, accelerate the research of fishery technology, actively develop the carbon sink fishery, and enhance the specialization of aquatic product processing.