Within the interior of the Yangtze Craton, the dome-like Huangling anticline exposes ca. 1000 km2 of Archaean basement and Neoproterozoic granitoid rocks in the Three Gorges region, providing a natural laboratory for studying the mechanism of intracontinental exhumation. Cretaceous shortening of the Qinling Orogen and Cenozoic reorganization of the Yangtze River have been considered by previous thermochronology studies to account for the two-phase exhumation of the Huangling anticline. However, little is known about when and how the batholithic rocks were exposed to the surface. To fully reveal the exhumation history of the Huangling anticline, we focus on the Cenozoic sedimentary record in the western Jianghan Basin, downstream of the Three Gorges, and examined spatio-temporal changes in sedimentation dynamic and provenance on the basis of sedimentary facies, palaeocurrents and clast compositions, as well as zircon U-Pb geochronology. Our results indicate continuous unroofing of the Huangling anticline since the Eocene and provide a solid evidence for first exposure of the Huangling batholith during the Neogene. Cenozoic exhumation of the Huangling anticline is synchronous with incision of the Three Gorges, indicating a mechanism of intracontinental exhumation due to Yangtze River reorganization through which the Middle Yangtze River was progressively captured by the Lower Yangtze River with locally increased erosion rates in the Three Gorges.