The Southern Ocean is a key regulator of global climate through its control of heat, carbon, freshwater, and nutrient exchange between the poles and the equator. Here, we investigate the spatial and volume changes in Antarctic Intermediate Water and Subantarctic Mode Water over the past 21,000 years using an atmosphere–ocean–sea ice synchronously coupled Community Earth System model. Our findings show that Southern Ocean regions of deeper mixed layer depths closely overlap with the strong Southern Hemisphere westerly winds, highlighting their role in intermediate and mode water formation. From Heinrich Stadial 1 to the early Holocene, both the Antarctic Intermediate Water and Subantarctic Mode Water reorganized, expanding to nearly 2.4 times their previous depths while also becoming warmer, fresher, and larger in volume. In contrast, both the water masses shoaled and contracted during Heinrich Stadial 1. Between the Heinrich Stadial 1 and the early Holocene, both the permanent sea ice margin and the Subantarctic Mode Water surface distribution region migrated poleward, with the latter exhibiting a twofold greater shift (~10°) relative to the former (~5°). These findings reveal a strong coupling between Antarctic sea ice distribution, Southern Hemisphere westerly wind strength, and the formation and distribution of Antarctic Intermediate Water and Subantarctic Mode Water, highlighting their role in global ocean circulation and climate change.