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Molecular biomarkers (e.g., isoprenoid glycerol dialkyl glycerol tetraethers (iGDGTs) and proxies, such as di-unsaturated to tri-unsaturated highly branched isoprenoids (D/T) ratio, total organic carbon, δ13C and ice-rafted debris (IRD)) were used to reconstruct the dominant phytoplankton (diatoms, dinoflagellates and coccolithophores), phytoplankton and zooplankton productivity, biological pump structure, and archaea assemblage (Euryarchaeota and Crenarchaeota) from a marine sediment core (D5-6) dated with 210Pb (1922–2012). We characterized the environmental response to sea ice variations/global warming off the eastern Antarctic Peninsula. The results showed that (1) the biomarkers brassicasterol (average = 519.79 ng·g?1), dinosterol (average = 129.68 ng·g?1) and C37 alkenones (average = 40.53 ng·g?1) reconstructed phytoplankton (average = 690.00 ng·g?1) and zooplankton (cholesterol average = 669.25 ng·g?1) productivity. The relative contribution to productivity by different phytoplankton groups was diatoms > dinoflagellates > coccolithophores. This is consistent with field surveys showing that diatoms dominate the phytoplankton in waters adjacent to the Antarctic Peninsula. (2) The relative abundances of different highly branched isoprenoids reflected the contributions of sea ice algae and open water phytoplankton (D/T = 1.2–30.15). Phytoplankton productivity and sea ice showed a good linear relationship with a negative correlation, indicating that more open water during periods of warming and reduced sea ice cover led to an enhanced biological pump. (3) Over the past 100 years, phytoplankton productivity and zooplankton biomass increased. This trend was particularly evident in the last 50 years, corresponding to increased global warming, and showed a negative correlation with IRD and D/T. This suggests that with decreasing sea ice coverage in a warming climate, diatom biomass greatly increased. Coccolithophore/diatom values and the ratio of C37 alkenones to total phytoplankton productivity decreased, indicating the proportion of coccolithophores in the phytoplankton community decreased. The reduction in coccolithophores changes the phytoplankton assemblage and affects the overall efficiency of the biological pump and carbon storage. (4) The results also showed that the abundance of iGDGTs and archaea phyla (Euryarchaeota and Crenarchaeota) showed consistent changes over the past 100 years in response to global warming. Since 1972, trends in archaea, phytoplankton and zooplankton showed variations but a consistent decline. Whether their response to the changing climate off the Antarctic Peninsula involves interactions and influence among different marine biological groups remains an open question. As a result of global warming and reductions in Antarctic sea ice, the relative effectiveness of the Antarctic biological pump can significantly affect global ocean carbon storage.