Previously published research from the Kuqa Subbasin along northern margin of the Tarim Basin shows five tectonic-depositional phases from Triassic to Neogene time. In order to reveal additional detailed information on the nature of provenance terrains and tectonic attributes since late Mesozoic time, five typical sandstone samples from Jurassic–Neogene strata were collected for U–Pb dating of detrital zircons. Geochronological constitution of detrital zircons of the Middle Jurassic sample is essentially unimodal and indicates major contributions from the South Tian Shan even Yili–Central Tian Shan, wherein most 370–450 Ma zircons probably resulted from tectonic accretion events between the Yili–Central Tian Shan block and South Tian Shan Ocean during Silurian and Devonian time, with sandstone provenance tectonic attributes of passive continental margin. The Lower Cretaceous sample shows a complicated provenance detrital zircon signature, with new peak ages of 290–330 Ma as well as 370(or 350)–450 Ma showing evident arc orogenic provenance tectonic attribute, probably reflecting a new provenance supply that resulted from denudation process whthin the South Tian Shan and South Tian Shan suture. There are no obvious changes within age probability spectra of detrital zircons between the Cretaceous and early Paleogene samples, which suggests that similar provenance types and basin-range framework continued from Cretaceous to Early Paleogene time. However, unlike the Cretaceous and early Paleogene samples, an age spectra of the Miocene sample is relatively unimodal and similar to that of the Pliocene sample, with peak ages ranging between ∼392 and ∼458 Ma older than the comparable provenance ages (peak ages about 370–450 Ma) of the Middle Jurassic and Lower Cretaceous samples. Therefore, we conclude that the South Tian Shan was rapidly exhumated and the southern South Tian Shan had become the main source of clastics for the Kuqa Subbasin since the Miocene epoch.