Fission-track dating was conducted on zircons and apatites from 11 cores of the upper Xiaganchaigou Formation and lower Shangganchaigou Formation (northwestern Qaidam Basin). The obtained apatite fission-track age is 3.1–61.9 Ma, and the zircon fission-track age is 49.2–123.5 Ma. Although the average apatite age is consistent with ages predicted from the stratigraphy, nine of the 11 apatite fission-track ages have \(\hbox {P}(\upchi ^{2}) < 5\%\), indicating that the grains experienced heterogeneous annealing after sedimentation. The average zircon age is greater than that indicated by stratigraphy, and all eight zircon fission ages have \(\hbox {P}(\upchi ^{2})>5\%\), exhibiting consistent characteristics and indicating that zircons retain provenance age information after burial. From the zircon and apatite ages, the fission-track length distribution, and the geological setting, the northwestern Qaidam Basin has experienced two tectonothermal events since the Late Mesozoic, at \(39.1 \pm 9.3\) to \(133.7\,\pm \,6.6\,\hbox {Ma}\) and \(1.2 \pm 0.6\) to \(32.0\,\pm \,3.0\,\hbox {Ma}\). The earlier (39.1–133.7 Ma) tectonothermal event resulted from the initial collision of the Indian and Eurasian plates. As a consequence of the collision, the Altyn Tagh fault, which forms the northwestern boundary of the Qaidam Basin, began to develop. Subsequently, uplift of the Altyn Tagh mountains began and the northwestern depression of the Qaidam Basin started to form. The later (1.2–32.0 Ma) tectonothermal event resulted from further collision of the Indian and Eurasian plates along the Yarlung Tsangpo suture zone. Strata in the Qaidam Basin were further deformed by transpression in this period and this period played a crucial role in petroleum accumulation.
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