Ocean mesoscale flows significantly influence nutrient distribution and biological productivity, yet the scarcity of eddy‐permitting observational data sets and climate modeling hinders understanding their role in carbon sequestration. Using an eddy‐resolving global simulation, this study investigates the significance of ocean mesoscales in air‐sea carbon dioxide (CO₂) exchange. Results show over 30% of CO₂ flux variance in energetic regions attributed to flows with horizontal scales smaller than 2-degree. Mesoscale flows can drive accumulative CO₂ flux that is either a net carbon sink or source depending on region, with magnitudes on the order of 10⁵ tonnes of carbon per year. Variations in this mesoscale‐related CO₂ flux are correlated with local relative vorticity and the background gradient of ocean partial pressure of CO₂. This analysis underscores the importance of considering ocean mesoscales in monitoring carbon flux, highlighting the need to explore the influence of increasing eddy activity on carbon uptake in a changing climate.