Several recent observation-based studies suggest that ocean anthropogenic carbon uptake has slowed down due to the impact of anthropogenic forced climate change. However, it remains unclear if detected changes over the recent time period can really be attributed to anthropogenic climate change or to natural climate variability (internal plus naturally forced variability). One large uncertainty arises from the lack of knowledge on ocean carbon flux natural variability at the decadal time scales. To gain more insights into decadal time scales, we have examined the internal variability of ocean carbon fluxes in a 1000-yr long preindustrial simulation performed with the Earth System Model IPSL-CM5A-LR. Our analysis shows that ocean carbon fluxes exhibit low-frequency oscillations that emerge from their year-to-year variability in the North Atlantic, the North Pacific, and the Southern Ocean. In our model, a 20-yr mode of variability in the North Atlantic air-sea carbon flux is driven by sea surface temperature variability and accounts for ~40% of the interannual regional variance. The North Pacific and the Southern Ocean carbon fluxes are also characterized by decadal to multi-decadal modes of variability (10 to 50 yr) that account for 30–40% of the interannual regional variance. But these modes are driven by the vertical supply of dissolved inorganic carbon through the variability of Ekman-induced upwelling and deep-mixing events. Differences in drivers of regional modes of variability stem from the coupling between ocean dynamics variability and the ocean carbon distribution, which is set by large-scale secular ocean circulation.