Utilizing the molecular biomarkers of organic matter in marine sediments from the Antarctic Peninsula (D1-7) and adjacent waters of the South Orkney Islands (D5-6), the ecological relationships implicit in the reconstructed variations of planktonic productivity and population structure are examined in relation to the Biological Pump (BP)/Microbial Carbon Pump (MCP), as well as the efficiency of marine carbon sinks and storage. Over the past century, a series of molecular biomarkers in sediment cores has exhibited significant changes, reflecting substantial spatiotemporal evolution in upper ocean planktonic productivity/community structure and sedimentary carbon reservoirs. These changes are indeed linked to global climate variability. The research findings are as follows: (1) Based on the characteristics of molecular composition and chromatographic peak patterns of biomarker compounds, as well as parameters such as Main Peak Carbon (MH), Light Hydrocarbons/Heavy Hydrocarbons (L/H), Bacterial-Algal Ratio (nC₁₅ + nC₁₇ + nC₁₉), Large Phytoplankton Ratio (nC₂₁ + nC₂₃ + nC₂₅), and carbon preference index (CPI), it is evident that the primary source of sedimentary carbon is marine-derived organic carbon. Marine organisms serve as natural carbon sinks for carbon fixation and storage. (2) The sediments from the D5-6 region exhibit high organic matter enrichment, primarily influenced by factors such as higher surface water productivity, higher sedimentation rates (average of 0.19 cm/a), shallower water depths (385 m), and a reducing sedimentary environment (average Pr/Ph value of 0.95). These conditions favor the transport of Particulate Organic Carbon (POC) from the ocean surface to the deep sea via the Biological Pump (BP) process, facilitating rapid burial and storage. In contrast, sediments from the D1-7 region, characterized by greater water depths (1 100 m) and lower sedimentation rates (0.07 cm/a, experience degradation of carbonaceous compounds during sedimentation processes and subsequent oxidative degradation in an oxic environment (average Pr/Ph value of 1.22). Both processes are unfavorable for carbon sequestration in sediments. However, the control factor determining carbon preservation in sediments may predominantly be sedimentation rate. (3) Over the past century, the total abundance of zooplankton, primary productivity of phytoplankton, and biomass of diatoms and dinoflagellates in the waters near the Antarctic Peninsula and the South Orkney Islands have shown an increasing trend, while the biomass and proportion of coccolithophores have decreased (particularly evident near the Antarctic Peninsula). This indicates a declining trend in the effectiveness of the calcium carbonate pump while the silica pump dominated by diatoms is strengthening. The relative strengths of these two processes largely determine the structure and efficiency of the biological pump, as well as the proportion of organic and inorganic carbon transported to marine sediments. (4) The trends in molecular biomarker variations in the two sediment cores show certain comparability overall, with distinct stages. Following interdecadal shifts (since 1972), the waters near the South Orkney Islands experienced a significant increase in zooplankton abundance from a depth of 5-6 cm beginning in 1982. Particularly, during the periods of 1997 and 2012, zooplankton abundance witnessed a dramatic increase, indicating rapid changes in planktonic community structure under the backdrop of global warming. Variations in both decreased primary productivity of phytoplankton and increased zooplankton abundance contribute to significant uncertainties in the changes in the strength of the biological pump (enhancement/weakening). (5) In contrast, over the past century, the productivity of phytoplankton/diatoms and dinoflagellates in the waters near the Antarctic Peninsula has gradually increased, while microbial productivity/ancient archaeal biomass has decreased. This suggests a weakening of microbial carbon sequestration intensity, indicating a decrease in the efficiency of the microbial carbon pump (MCP). This underscores the crucial role of global warming in the fluctuations of phytoplankton productivity/biomass in marine waters. The biomass and composition characteristics of planktonic communities directly affect the transport of organic carbon in the upper water column and the efficiency of carbon sequestration in the MCP. As the largest carbon sink in the global ocean, the carbon sequestration capacity of the Antarctic may be diminishing.