Reactivation of the Qinling Orogen since the Late Jurassic has been controlled by the combined effects of the convergence between the South and North China blocks, the subduction of the Pacific Plate, and the northeastward expansion of the Tibetan Plateau. In this study, we present new apatite (U–Th)/He ages from a vertical transect in the Fenghuang Shan located in the North Daba Mountains, where rapid cooling at ∼95-90 Ma is identified. Inverse thermal history modeling results reveal another pulse of accelerated exhumation at ∼50 Ma. In addition, we analyzed longitudinal profiles of rivers draining the northern flank of the Fenghuang Shan and identified knickpoints that break channels into gentle upstream and steep downstream segments. We deduce that these knickpoints were initiated by an increase in the mountain-bounding fault throw, based on nearly constant chi values (an integral to the upstream drainage area distribution) and a reliance of knickpoints’ retreat distances on catchment areas. Assuming a linear slope exponent and erodibility of 10−6 m0.1/a, we estimated knickpoint ages to be ∼5.7 ± 1.7 Ma. We interpret the Late Cretaceous cooling as a result of lithospheric extensional collapse following the Late Jurassic intra-continental compression between the North and South China blocks. The early Cenozoic exhumation might relate to the active normal faulting, as a far-field response to the west Pacific back-arc extension. The expansion of the NE Tibetan Plateau may have triggered the late Miocene uplift of the mountain range. The multiple episodes of tectonic events in the Fenghuang Shan might correspond to various geodynamic regimes on the tectonic evolution in the Qinling Orogen.