We collected two lake sediment cores (MC and DM) from the East Antarctic region for analysis of biogenic silica and other biogeochemical parameters (e.g., organic matter, C, N, S, H). Based on synthetically comparative research, we focused on the potential application of biogenic silica (BSi) for the reconstruction of paleo-primary productivity in the East Antarctic lakes. Analytical results showed that a large number of diatoms were well preserved in the freshwater lake sediments, and that concentrations of biogenic silica displayed notable fluctuations over different water depths. The content of biogenic silica had a consistent profile over water depth, and this pattern changed with organic matter, reflecting their potential as eco-environmental proxies. Low levels of BSi and organic matter indicated reduction of lake algal production, and corresponded to decreased lake primary productivity. Due to the fragile ecosystem state and limited contribution of terrestrial organic matter in the East Antarctic lakes, the contents of biogenic silica in the lacustrine sediments can sensitively indicate the evolutionary history of paleo-primary productivity. Overall, BSi is an ideal proxy for the reconstruction of past eco-environmental change recorded in the lacustrine sediments on East Antarctica. We collected two lake sediment cores (MC and DM) from the East Antarctic region for analysis of biogenic silica and other biogeochemical parameters (eg, organic matter, C, N, S, H). Based on synthetically comparative research, we focused on the potential application of biogenic silica (BSi) for the reconstruction of paleo-primary productivity in the East Antarctic lakes. Analytical results showed that a large number of diatoms were well preserved in the freshwater lake sediments, and that concentrations of biogenic silica displayed notable fluctuations over different water depths. The content of biogenic silica had a consistent profile over water depth, and this pattern changed with organic matter, reflecting their potential as eco-environmental proxies. Low levels of BSi and organic matter indicated reduction of lake algal production, and corresponded to decreased lake primary productivity. Due to the fragile ecosystem state and limited contribution of terrestrial organic matter in the East Antarctic lakes, the contents of biogenic silica in the lacustrine sediments can be sensitive to the evolutionary history of paleo-primary productivity. Overall, BSi is an ideal proxy for the reconstruction of past eco-environmental change recorded in the lacustrine sediments on East Antarctica .