Changes in deep-water ventilation and surface biogenic pump may have played a prominent role in the atmospheric CO2 variability. However, how these circulations and the biological pump have varied remains poorly understood, and further detailed analysis is needed, especially for interhemispheric comparison. Here, we present high-resolution proxy data on the variability of biological productivity, bottom water current speed, and upwelling changes for the abyssal northwestern Pacific Ocean spanning 20 to 60 kyr ago. We found that enhanced surface productivity correlates with the timing of North Atlantic Heinrich Stadial and interpret this as a result of a combination of increased nutrient supply to the euphotic zone and intensified westerly winds causing dust fertilization. Based on our proxy data-model comparison, we infer enhanced deep-water ventilation in the Southern Ocean to drive pCO2 variability on millennial timescales in support of a bipolar carbon cycle seesaw between the Northern and Southern Hemisphere. Overall, our findings demonstrate that deep ocean carbon storage and degassing are modulated by atmosphere and ocean ventilation through the nonlinear interplay of the two hemispheres.