• Mesozoic sediments within the Qilian Shan orogenic belt transitioned from a “sink” to a “source” before the Oligocene . • Obvious provenance change occurred at ∼22 Ma in the Subei Basin, an intermontane basin within the Qilian Shan orogenic belt. • The southern Qilian Shan orogenic belt underwent deformation in the earliest Miocene and middle-late Miocene. • Recycled Oligocene sediments inside the basin became the main provenance at ∼9 Ma. • The Qilian Shan orogenic belt underwent three stages of tectonic events that began in the early Cenozoic shortly after the India-Eurasia collision. Timing and patterns of the Cenozoic deformation of the Qilian Shan orogenic belt (QSOB) in the northern Tibetan Plateau are key to elucidating the mechanism(s) of plateau growth but remain matters of debate. The Oligocene-Miocene sediments in the Subei Basin, an intermontane basin situated at the junction of the central and southern QSOB, provide direct insight into the Cenozoic deformation of the QSOB. Here, a comprehensive provenance study based on detrital zircon geochronology, paleocurrents, conglomerate components and sedimentary facies in the Subei Basin demonstrates that this region experienced three stages of tectonic events during the Cenozoic. (1) Oligocene strata contain zircons of 200–300, 400–500, 700–1000, 1600–2000 and 2400–2700 Ma, indicating primary derivation from recycled Mesozoic sedimentary rocks in the QSOB and suggesting early Cenozoic deformation in this region. (2) One sample (21.5 Ma) yields similar age populations to those of Oligocene samples, except for the complete disappearance of 200–300 Ma zircons as a result of the widespread deformation of the QSOB. (3) Two samples (18.5–13.6 Ma) show a unimodal age cluster at 400–500 Ma, while one sample (9 Ma) contains zircon ages similar to those of Oligocene samples, indicating tectonic uplift of the southern QSOB in the middle-late Miocene, which is also recorded by the sedimentary transition from fluvial to alluvial fan. Based on these findings and those of previous studies, we suggest that the entire QSOB has undergone multistage tectonic events since the early Cenozoic due to far-field effects associated with the India-Eurasia plate collision and the continued convergence.