The Greater Khingan Mountains (GKMs) are a prominent orogenic zone in Northeast Asia that offers significant insights into the evolution of the Mongol-Okhotsk Ocean and the Pacific Ocean during the Phanerozoic. A comprehensive study integrating a low-temperature thermochronology analysis pertaining to the Greater Khingan area and its associated basins has been conducted. Apatite fission-track (AFT) tests conducted on detrital samples from the GKMs in Northeast China have yielded central ages ranging from 260 to 62 Ma. Two-dimensional thermal history inversion modeling and three-dimensional numerical simulations were used to investigate the GKMs' thermal history, revealing at least two distinct tectonic cooling and exhumation events: one occurring between 147 and 70 Ma and another around 35 Ma. The fission-track age groups of the GKMs, Hailar-Erlian Basin, and Mohe Basin bear some resemblance (>105 Ma), but the results from the Songliao Basin are unique. This implies that the Songliao Basin and the GKMs were likely under the influence of different tectonic domains during this period, while AFT age peaks between 105 and 45 Ma, indicating the basin-mountain systems were likely influenced by a unified Paleo-Pacific plate process, which prevailed from about 105 Ma. The 147–70 Ma cooling event can be attributed to the combined effects of the compression orogeny, resulting from the closure of the Mongol-Okhotsk Ocean during the Early Cretaceous and the extension orogeny triggered by the subduction of the Paleo-Pacific Ocean during the early Late Cretaceous. Since approximately 35 Ma, the increase in Pacific plate subduction speed may have established a post-arc extensional tectonic environment in the GKMs that has persisted until now.