Abstract The widespread appearance of intermontane basins in the northern Tibetan Plateau herald the outward expansion of tectonic deformation into the sedimentary basins. When and how the basins have been deformed and segmented, however, remain still unexplored. The Qaidam basin, the biggest intermontane basin in Tibet, archives up to 20 km‐thick sedimentary succession ranging in age from Paleozoic to Cenozoic. To tackle this issue, here we present a relatively large apatite fission track data set, coupled with detailed structural observations, for the Paleozoic‐Cenozoic strata of the fold‐thrust belt of the northern Qaidam Basin. Our results indicate that the activity of a typical pop‐up structure, consisting of foreland‐verging and antithetic high‐angle reverse faults, led to the rapid exhumation of 2–3 km‐thick basin‐margin strata since 10‐7 Ma. This tectonic event coincidently induced a major sediment recycling event observed at multiple sedimentary sections within the basin, as well as abrupt variations in lithology, grain size, and magnetic susceptibility value at ca. 8 Ma. The source‐to‐sink reconstruction, for the first time ever, offers evidence for a syntectonic intrabasinal sediment recycling. This late Miocene activity has also been observed within other subordinate basins, suggesting a nearly synchronous onset of compressional deformation propagating into the basins of northern Tibet since ∼8 Ma. A slowing extrusional tectonics under restricted boundary conditions may explain this coeval crustal thickening and uniform uplift of northern Tibet.