Antarctic climate warming and atmospheric CO2 rise during the last deglaciation may be attributed in part to sea ice reduction in the Southern Ocean. Yet, glacial-interglacial Antarctic sea ice dynamics and underlying mechanisms are poorly constrained, as robust sea ice proxy evidence is sparse. Here, we present a molecular biomarker-based sea ice record that resolves the spring/summer sea ice variability off East Antarctica during the past 40 thousand years (ka). Our results indicate that substantial sea ice reduction culminated rapidly and contemporaneously with upwelling of carbon-enriched waters in the Southern Ocean at the onset of the last deglaciation but began at least ~2 ka earlier probably driven by an increasing local integrated summer insolation. Our findings suggest that sea ice reduction and associated feedbacks facilitated stratification breakup and outgassing of CO2 in the Southern Ocean and warming in Antarctica but may also have played a leading role in initializing these deglacial processes in the Southern Hemisphere.