The Harlik Mountain is in the easternmost part of the Tian Shan and is a prime example of an intracontinental orogenic belt. Several studies have used low‐temperature thermochronology to understand the uplift history of this range. However, complicated structures have a profound impact on the study of the tectonic evolution of the Harlik Mountain during the Mesozoic‐Cenozoic. Here, we refine the structural characteristics of the Harlik Mountain and then acquire the detailed thermal histories in different parts of the range. Through field observations, we demonstrate that the brittle Harlik Fault experienced two activities, including early normal faulting and late right‐lateral strike‐slip normal faulting. In particular, geomorphic and river analyses indicate that the topography of the Harlik Mountain was significantly influenced by faults. Combined with the thermochronological data from previous studies, thermal history modelling based on our new data on the Harlik Mountain suggest three fast cooling phases in the 128–110 Ma, 70–55 Ma, and 50–35 Ma. The first and the third cooling phases were associated with fault activities and the second cooling phase was related to regional denudation. The first phase of faulting, in the late Early Cretaceous, may be caused by stress relaxation after the Cimmerian collision. The second phase of faulting was likely to relate to local stress adjustment from the India‐Eurasia collision during the Eocene to Oligocene. Moreover, Late Cretaceous to Palaeocene regional cooling was probably affected by the collision of the Karakoram Block with Eurasia.