Ice core measurements show diverse atmospheric CO2 variations—increasing, decreasing or remaining stable—during millennial-scale North Atlantic cold periods called stadials. The reasons for these contrasting trends remain elusive. Ventilation of carbon-rich deep oceans can profoundly affect atmospheric CO2, but its millennial-scale history is poorly constrained. Here we present a well-dated high-resolution deep Atlantic acidity record over the past 150,000 years, which reveals five hitherto undetected modes of stadial ocean ventilation with different consequences for deep-sea carbon storage and associated atmospheric CO2 changes. Our data provide observational evidence to show that strong and often volumetrically extensive Southern Ocean ventilation released substantial amounts of deep-sea carbon during stadials when atmospheric CO2 rose prominently. By contrast, other stadials were characterized by weak ventilation via both Southern Ocean and North Atlantic, which promoted respired carbon accumulation and thus curtailed or reversed deep-sea carbon losses, resulting in diminished rises or even declines in atmospheric CO2. Our findings demonstrate that millennial-scale changes in deep-sea carbon storage and atmospheric CO2 are modulated by multiple ocean ventilation modes through the interplay of the two polar regions, rather than by the Southern Ocean alone, which is critical for comprehensive understanding of past and future carbon cycle adjustments to climate change.