Partially due to lack of structural and sedimentary records to constrain the Jurassic-to-Cretaceous evolution, there was a missing process here in the eastern margin of Tibetan Plateau as it changed from the Paleo-Tethyan to Neo-Tethyan regime. Based on the analysis of 125 thermochronology ages (U/Pb, 40Ar/39A, 87Rb/86Sr, FT, U-Th/He) of igneous rocks from the eastern margin of Tibet, we propose a multisystem thermochronology approach to restore the cooling and emplacement of granites and decipher the missing process. Our integrated study suggests that a key Late Cretaceous (about 100Ma) tectonic change from the Paleo-Tethyan to Neo-Tethyan regime took place there. In the Late Triassic period, the initial emplacement of granite in the Songpan-Ganzi Fold Belt (SGFB) was characterized by a decrease in emplacement age and depth from west to east, and from north to south. Subsequently, all were followed by a very long period of slow cooling, which was followed by a rapid emplacement of about 100Ma. The intensive granite emplacement took place all over except northeastern SGFB, with a decrease in emplacement depth from west to east, which was linked with the far-field effect of Lhasa-Qiangtang collision. After this episode, the cooling history of granite in SGFB had a rapid emplacement on the subsurface under the control of the Neo-Tethyan regime. This process has control of the post Late Cretaceous regional magmatic activity and tectonics, as well as the sedimentary response in Sichuan and Xichang basin.