Crustal accretion at mid-ocean ridges governs the creation and evolution of the oceanic lithosphere. Generally accepted models1–4 of passive mantle upwelling and melting predict notably decreased crustal thickness at a spreading rate of less than 20 mm year−1. We conducted the first, to our knowledge, high-resolution ocean-bottom seismometer (OBS) experiment at the Gakkel Ridge in the Arctic Ocean and imaged the crustal structure of the slowest-spreading ridge on the Earth. Unexpectedly, we find that crustal thickness ranges between 3.3 km and 8.9 km along the ridge axis and it increased from about 4.5 km to about 7.5 km over the past 5 Myr in an across-axis profile. The highly variable crustal thickness and relatively large average value does not align with the prediction of passive mantle upwelling models. Instead, it can be explained by a model of buoyant active mantle flow driven by thermal and compositional density changes owing to melt extraction. The influence of active versus passive upwelling is predicted to increase with decreasing spreading rate. The process of active mantle upwelling is anticipated to be primarily influenced by mantle temperature and composition. This implies that the observed variability in crustal accretion, which includes notably varied crustal thickness, is probably an inherent characteristic of ultraslow-spreading ridges.