Marine ranching, through the establishment of artificial reefs and mariculture facilities, effectively promotes the proliferation of marine organisms in an area. It is a promising strategy for enhancing the carbon sink function of fishery ecosystems, thereby contributing significantly to climate change mitigation. Currently, most research on carbon sequestration in marine ranching focuses on artificial reef areas, but studies on the carbon sequestration potential of different functional zones across the entire system remain limited, especially regarding their dynamic changes at high spatial and temporal resolutions and their relationship with environmental factors. Therefore, this study integrated in situ sampling with satellite remote sensing and conducted multi-seasonal and multiple-cruise surface water sampling to analyze chlorophyll-a concentration (Chl-a), sea surface temperature (SST), and other environmental factors. Comparisons between Chl-a, SST data, and remote sensing products validated the applicability of satellite data for monitoring long-term marine trends. The Vertically Generalized Production Model (VGPM) was used to estimate the net primary productivity (NPP) of phytoplankton, quantifying their carbon sequestration capacity and analyzing the spatiotemporal variations of Chl-a concentration and phytoplankton carbon sequestration across different functional zones. The Generalized Additive Model (GAM) was applied to examine the relationships between environmental factors and carbon sequestration intensity and to assess the impact of marine ranching on the carbon sink capacity. Additionally, by comparing the changes in Chl-a concentration before and after the construction of marine ranching, this study further analyzed its impact on the regional carbon sink capacity. The results showed that: (1) The trends of Chl-a concentration and sea surface temperature observed in both remote sensing and in situ data were largely consistent, validating the reliability of using remote sensing data to assess long-term trends in marine environments. (2) Following the establishment of the marine ranching, Chl-a concentration exhibited significant seasonal and spatial variability, characterized by an “M”-shaped double-peak pattern, with peaks occurring during the summer-to-fall and winter-to-spring transition periods. The overall Chl-a concentration was significantly higher than both pre-establishment levels and those in the control area. (3) Carbon sequestration intensity also showed notable spatiotemporal distribution differences, featuring a pronounced peak in summer (June). The overall carbon sequestration intensity was significantly higher than that of the control area, with a total annual carbon sequestration of 1.85×106 kgC, indicating that marine ranching contributes significantly to enhancing the regional carbon sink capacity. (4) In the optimal GAM model, pH, silicate, dissolved oxygen, salinity, and latitude were identified as significant factors influencing carbon sequestration intensity. Notably, silicate promoted carbon sequestration within a certain concentration range. This study emphasizes the important role of artificial reefs and aquaculture infrastructure in enhancing carbon sequestration by promoting phytoplankton growth and altering hydrodynamic conditions. The findings suggest that future research should focus on optimizing marine ranching practices to maximize carbon sequestration effects. Future studies should explore the interactive effects of multiple environmental factors, examine the roles of different functional zones within marine ranching, and develop improved management strategies to enhance the carbon sink functions of these ecosystems. Furthermore, the integration of satellite remote sensing with in situ sampling provides a comprehensive approach to understanding the spatiotemporal dynamics of carbon sequestration in marine ecosystems. This method enables high-resolution monitoring of carbon fluxes, making it an important tool for assessing the effectiveness of marine ranching and its contribution to the global carbon budget.