Functional zoning constitutes a critical bridge connecting scientific understanding with actionable policy implementation. Within the critical domain of climate change mitigation, marine carbon sink functional zoning demonstrates significant potential for elucidating spatial and temporal patterns of marine carbon sequestration, enhancing the accuracy of carbon sink accounting, and providing robust scientific support for the fulfillment of Nationally Determined Contributions. However, dedicated study specifically addressing the theoretical foundations and methodological frameworks for marine carbon sink functional zoning remains notably scarce, representing a significant gap in both scientific literature and practical ocean management. This study directly addressed this study void by establishing a comprehensive theoretical and technical framework for marine carbon sink functional zoning. First, we conducted a thorough review of the historical evolution of theories and methods pertaining to carrying capacity and development suitability. This review integrated theoretical paradigms from multiple disciplines-including marine science, geography, and urban and rural planning-and analyzes their practical applications within territorial spatial planning and broader marine spatial management contexts. Subsequently, in accordance with the principle of marine sustainable development, we clarified the natural and social attributes essential to marine carbon sink. Assessing the functional importance and vulnerability of marine carbon sink based on their natural attributes, alongside evaluating the development suitability for human interventions aimed at augmenting carbon sequestration based on their social attributes. This integrated analysis enables the proposal of a scientifically rigorous, systematically structured, and inherently management-oriented theoretical framework specifically designed for marine carbon sink functional zoning. Further refining the practical application, we proposed a targeted zoning methodology explicitly grounded in the key functional characteristics of marine carbon sink. Utilizing the threshold method and leveraging assessments of carbon sink carrying capacity and development suitability, this methodology classifies marine spatial units by delineating three critical boundaries: source-sink boundaries (demarcating areas of net carbon uptake versus release), ecological boundaries (identifying limits to prevent ecosystem degradation), and suitability boundaries (defining areas viable for managed enhancement activities). Finally, the study articulated crucial application directions for marine carbon sink functional zoning within the overarching goal of achieving carbon neutrality. These applications encompass enhancing the precision of marine carbon sink accounting, guiding the development of effective carbon sink enhancement strategies, informing marine spatial planning decisions, and supporting integrated ocean management approaches. Collectively, the developed framework provides an indispensable scientific basis and practical technical support. It empowers policymakers and resource managers to strategically harness the full potential of marine ecosystems within global climate mitigation efforts.