Abstract The Tianshan Mountains, which formed through the prolonged and complex subduction-accretion of the paleo-Asian ocean, experienced multiple widespread erosions and reactivations during the Mesozoic-Cenozoic period. Thus, the Tianshan has become a crucial area to explore the process and mechanism of intracontinental orogeny. The Harlik Mountain located in the easternmost part of Tianshan has special significance in revealing crustal deformation and far-field stress propagation. In this study, we use the apatite (U-Th)/He method to investigate the near-surface exhumation process of Harlik Mountain, which is the result of tectonic events and erosion. The apatite (U-Th)/He data and thermal history modeling reveal three enhanced exhumation events in the Harlik Mountain, i.e., the early Cretaceous, the late Cretaceous-Paleocene, and the middle Eocene. These events are consistent with the exhumation patterns observed throughout the entire Tianshan. Notably, the exhumation rate and amplitude in the early Cenozoic period were significantly higher in the Harlik Mountain compared with the Mesozoic period. Our findings reveal that the exhumation of the Harlik Mountain and the entire Tianshan displayed pronounced spatial-temporal variations throughout the Mesozoic-Cenozoic period. These variations can be attributed to the combined effect of uneven northward compression of the southern Asian margin, the heterogeneous rheological properties of the lithosphere, and the complex structure of the Tianshan.