The Southern Ocean waters exchange freshwater, nutrients, carbon, heat, and salt to the Equator and influence the global carbon budget. Therefore, it is essential to understand the variations in Southern Ocean circulation during the last deglacial period to comprehend its changes with climate change. This modeling study employs a fully coupled Earth system model to investigate the Southern Ocean Subantarctic Mode and Antarctic Intermediate Waters distribution during the last deglaciation. The simulation shows that the Southern Hemisphere’s low-level winds overlap with the zone of maximum mixed layer depth, signifying the impact of westerlies in the Southern Ocean waters. The results indicate that the Southern Ocean Subantarctic Mode and Antarctic Intermediate Waters are fresher, warmer, and about 2.4 times deeper during the early Holocene compared to the Heinrich-1. The simulated Antarctic sea ice boundary (ocean surface area covered with more than five percent sea ice fraction) overlaps with the poleward edge of the Antarctic Intermediate Waters, and the Southern Ocean mixed layers. Additionally, the simulated quasi-permanent sea ice boundary (ocean surface area covered with more than eighty percent sea ice fraction) and the zone of Subantarctic Mode and Antarctic Intermediate Waters shifted polewards by about 5° and 10°, respectively, during the early Holocene compared to the Heinrich-1. Therefore, our study highlights a close link between the Antarctic sea ice distribution and the Southern Ocean Subantarctic Mode and Antarctic Intermediate Waters during the last deglacial period.