Apatite fission-track (AFT) tests of clastic samples from the Greater Khingan Mountains (GKM) in China show a center age of 260–62 Ma. Thermal modeling of observed fission-track-length distributions shows three stages of rapid cooling that may have been caused by extensions between 130 and 94 Ma, 30 and 15.3 Ma, and 45 and 0 Ma, and a heating event that may have been caused in part by changes in the subduction direction of the Pacific plate between 64 and 45 Ma. The cumulative exhumation since the Early Cretaceous, is approximately 3 km. The steady-state terrain model in the three-dimensional numerical simulation is highly consistent with the time and rate of the two-dimensional thermal history simulation for the Early Cretaceous exhumation event. The cooling age clusters of ~160 to 100 Ma are similar in the GKM and Hailar-Erlian Basins. This correlation provides a basin–mountain link for the two tectonic domains. Such a basin–mountain coupling lasted through 100–42 Ma, as supported again by the shared cooling ages of samples from the GKM and detritus from the range-bounded basins on the two sides of the mountain range. We interpreted the 130–94 Ma cooling event recorded in the GKM as a result of crustal thickening in response to the closure of the Mongolia-Okhotsk Ocean. An increase in the subduction velocity of the Pacific plate since ca. 45 Ma may have created a post-arc extensional tectonic setting that has prevailed to the present in the GKM.