Atmospheric carbon dioxide (CO2) concentration during glacial periods is known to be considerably lower than during interglacial periods. However, previous studies using an ocean general circulation model (OGCM) fail to reproduce this. Paleoclimate proxy data of the Last Glacial Maximum indicate high salinity (>37.0 psu) and long water mass residence time (>3,000 years) in the Southern Ocean, suggesting that salinity stratification was enhanced and more carbon was stored there. Reproducibility of salinity and water mass age is considered insufficient in previous OGCMs, which might affect the reproducibility of atmospheric CO2 concentration. This study investigated the role of increased stratification of the Southern Ocean in the glacial CO2 variation using an OGCM. We found that deep water formation in East Antarctica is required to explain high salinity in the South Atlantic. Saltier deep Southern Ocean resulted in increased atmospheric CO2 concentration against previous estimates. This is partly due to increased volume transport of Antarctic Bottom Water and associated decrease in the water mass age of the deep Pacific Ocean. On the other hand, weakening of vertical mixing contributed to increase of the vertical gradient of dissolved inorganic carbon and decrease of atmospheric CO2 concentration. However, we show that it is unable to explain all of the glacial CO2 variations by the contribution of the Southern Ocean. Our findings indicate that detailed understanding of the impact of enhanced stratification in the Southern Ocean on the Pacific Ocean might be crucial to understanding the mechanisms behind the glacial-interglacial ocean carbon cycle variations.