The Kuroshio Extension (KE) is the eastward extension of the Kuroshio, a major western boundary current in the Northern Hemisphere. The KE has long been recognized as a turbulent current system rich in large-amplitude meanders and energetic eddies. Not only is it a region where the largest interannual and longer time scale ocean circulation changes are detected in the North Pacific Ocean, the KE region is also known for absorbing large amounts of carbon dioxide (CO2) from the atmosphere, helping to slow climate change. However, the impact of interannual variability in the region's dynamic state and abundant mesoscale eddies on CO2 uptake remain uncertain. Using observation-based machine learning to estimate CO2 fluxes throughout the lifetimes of thousands of eddies, we show that anticyclonic eddies substantially enhance CO2 uptake on average, while cyclonic eddies marginally diminish it. This asymmetry yields an overall net increase in CO2 absorption by 9.98 ± 2.28% in the KE. Also, utilizing observational data and a state-of-the-art global ocean biogeochemistry model that assimilates both physical and biogeochemical observations, we reveal that the KE bimodal states substantially modulate sea-air CO2 flux. During the KE stable state, oceanic CO2 uptake intensifies due to lateral divergence of dissolved inorganic carbon (DIC) within the mixed layer and increased surface wind speed. The finding suggests a potential underestimation of the ocean's capacity for carbon sequestration because of insufficient incorporation of eddies in current observations, emphasizing the need for expanded monitoring in eddy-rich, undersampled regions.