The Zoige depression is an important depocenter within the northeast Songpan-Ganzi flysch basin, which is bounded by the South China, North China and Qiangtang Blocks and forms the northeastern margin of the Tibetan Plateau. This paper discusses the sediment provenance and Mesozoic-Cenozoic evolution of the Zoige depression in the Songpan-Ganzi flysch basin, eastern Tibetan Plateau, using the detrital zircon U-Pb ages and apatite fission-track data from the Middle to Late Triassic sedimentary rocks in the area. The U–Pb ages of the Middle to Late Triassic zircons range from 260–280 Ma, 429–480 Ma, 792–974 Ma and 1800–2500 Ma and represent distinct source region. Our new results demonstrate that the detritus deposited during the Middle Triassic (Ladinian, T2zg) primarily originated from the Eastern Kunlun and North Qinling Orogens, with lesser contributions from the North China Block. By the Late Triassic (early Carnian, T3z), the materials at the southern margin of the North China Block were generally transported westward to the basin along a river network that flowed through the Qinling region between the North China and South China Blocks: this interpretation is supported by the predominance of the bimodal distribution of 1.8 Ga and 2.5 Ga age peaks and a lack of significant Neoproterozoic zircon. Since the Late Triassic (middle Carnian, T3zh), considerable changes have occurred in the source terranes, such as the cessation of the Eastern Kunlun Orogen and North China Block sources and the rise of the northwestern margin of the Yangtze Block and South Qinling Orogen. These drastic changes are compatible with a model of a sustained westward collision between the South China and North China Blocks during the late Triassic and the clockwise rotation of the South China Block progressively closed the basin. Subsequently, orogeny-associated folds have formed in the basin since the Late Triassic (late Carnian), and the study area was generally subjected to uplifting and cooling stages during 200–160 Ma, 90–120 Ma, 20–40 Ma and 10 Ma as evidenced by the apatite fission track data and the thermal history modeling. According to the regional background, we conclude that these stages are as follows, from oldest to youngest: the E-W extrusion across the entire Chinese mainland at the beginning of the Yanshanian period (200–160 Ma), the interaction among the North China, Yangtze and India plates during the Late Jurassic-Early Cretaceous, the collision between the Indian and Eurasian plates since the Paleogene, and the rapid uplift simultaneous with the formation of the Tibetan Plateau since 10 Ma.