The deep-ocean carbon cycle, especially carbon sequestration and outgassing, is one of the mechanisms to explain variations in atmospheric CO2 concentrations on millennial and orbital timescales. However, the potential role of subtropical North Pacific subsurface waters in modulating atmospheric CO2 levels on millennial timescales is poorly constrained. An increase in the respired CO2 concentration in the glacial deep-ocean due to biological pump generally corresponds to deoxygenation in the ocean interior. This link thus offers a chance to study oceanic ventilation and coeval export productivity based on redox-controlled sedimentary geochemical parameters. Here, we investigate a suite of geochemical proxies in a sediment core from the Okinawa Trough to understand sedimentary oxygenation variations in the subtropical North Pacific over the last 50 000 years (50 ka). Our results suggest that enhanced mid-depth western subtropical North Pacific (WSTNP) sedimentary oxygenation occurred during cold intervals and after 8.5 ka, while oxygenation decreased during the Bölling-Alleröd (B/A) and Preboreal. The enhanced oxygenation during cold spells is linked to the North Pacific IntermediateWater (NPIW), while interglacial increase after 8.5 ka is linked to an intensification of the Kuroshio Current due to strengthened northeast tradewinds over the tropics. The enhanced formation of the NPIW during Heinrich Stadial 1 (HS1) was likely driven by the perturbation of sea ice formation and sea surface salinity oscillations in the high-latitude North Pacific. The diminished sedimentary oxygenation during the B/A due to a decreased NPIW formation and enhanced export production, indicates an expansion of the oxygen minimum zone in the North Pacific and enhanced CO2 sequestration at mid-depth waters, along with the termination of atmospheric CO2 concentration increase. We attribute the millennial-scale changes to an intensified NPIW and enhanced abyss flushing during deglacial cold and warm intervals, respectively, closely related to variations in North Atlantic Deep Water formation.