A distinctive NNE trending belt of shortening structures dominates the topography and deformation of the eastern Sichuan Basin, ~300 km east of the Tibetan Plateau. Debate continues as to whether the structures resulted from Cenozoic eastward growth of the Tibetan Plateau. A low‐temperature thermochronology (AFT and AHe) data set from four deep boreholes and adjacent outcrops intersecting a branch of the shortening structures indicates distinctive differential cooling at ~35–28 Ma across the structure, where stratigraphy has been offset vertically by ~0.8–1.3 km. This result forms the first quantitative evidence for the existence of a late Eocene‐Oligocene phase of shortening in the eastern Sichuan Basin, synchronous with the early phase of eastward growth and extrusion of the Tibetan Plateau. Further, a compilation of regional Cenozoic structures reveals a Miocene retreat of deformation from the foreland basin to the hinterland areas. Such a tectonic reorganization indicates that Eocene to Miocene deformation in the eastern Tibetan Plateau is out‐of‐sequence and was probably triggered by enhanced erosion in the eastern Tibetan Plateau.