The Indian Ocean accounts for more than 20% of the global ocean volume, nearly comparable with the Atlantic, and possesses a unique hydrography characterized by turn-over entirely through exchange with the Southern Ocean, Pacific and Atlantic. Despite its volumetric and hydrographic importance, deep-water ventilation change of the Indian Ocean and its role in glacial-interglacial carbon cycle dynamics remains poorly constrained. Here, radiocarbon dates on 16 pairs of contemporaneous planktic and benthic foraminifera from one marine sediment core at the 90°E Ridge have been used to decipher past changes in the “radiocarbon ventilation age” of deep waters from the northeastern Indian Ocean basin over ~40 ka. The average apparent ventilation ages (i.e., Benthic-Atmosphere offsets) were approximately 2250, 2700, and 2540 yrs during the Holocene, last deglaciation, and last glaciation, respectively. Interestingly, the deep-water ventilation ages peaked (>3000 ¹⁴C yrs) during the Heinrich Stadial-1 (HS1), as recorded in the intermediate Arabian Sea and the intermediate Bay of Bengal as well. This may reflect the upwelling of “old carbon” from the deep to the intermediate layer of the Indian Ocean. The deep-water ventilation ages were roughly higher during the glacial period than in the Holocene, probably indicating weaker ventilation and greater carbon storage. These findings underline the significant role played by the Indian Ocean in carbon cycle evolution, particularly over the last glacial-interglacial cycle.