The Southern Ocean plays a crucial role in the global carbon cycle, ocean heat transport, and Antarctic ice dynamics. Investigating past variability in the Southern Ocean, including temperature and water masses distribution, can improve understanding of how this system may respond to current climate change. Isoprenoid glycerol dialkyl glycerol tetraethers (isoGDGT) can be used as an ocean temperature proxy and have been applied to sediments in the Southern Ocean to reconstruct past temperature variability. However, applications of current isoGDGT-based temperature indices are subject to substantial uncertainty in the Antarctic Zone. In this study, we propose a new isoGDGT-based index, the so-called Antarctic IsoGDGT Zonal (AIZ) index, as a zonal water mass tracer of the Antarctic Circumpolar Current (ACC) based on reanalysed Southern Ocean core-top data. We also found that the AIZ index exhibits a significant correlation with subsurface temperature (subST) south of the Polar Front, suggesting that it can be used as a temperature proxy in the Antarctic Zone (subST = 24.17 × AIZ − 1.45 (<em>R²</em> = 0.81,<em> n</em> = 134, <em>p</em> < 0.0001)). Applying the AIZ index to late Pleistocene sediment cores collected around the ACC zone confirms its reliability as a water mass tracer and temperature proxy in the Antarctic Zone. Our study highlights the high potential of isoGDGT for reconstructing palaeoceanographic conditions in the Southern Ocean.