As a sensitive marker of plate collision events, intraplate compressional deformation can be used to provide a unique regional perspective for the contemporaneous complicated tectonic evolution at the plate margin. Two regional intraplate deformation and uplift events of the late Middle Jurassic and Late Jurassic-Early Cretaceous in the Junggar Basin were revealed through seismic interpretation and geological profiles, and both of them correspond to unconformity in the sedimentary successions. Detrital zircons from Jurassic and Cretaceous strata in the eastern margin of Junggar Basin were selected for LA-ICP MS U-Pb dating. Combined with previous detrital zircon U-Pb dating data, a prominent, time-continuous group of syn-depositional detrital zircons has been discovered in the Jurassic-Cretaceous strata of the Junggar basin, and their discontinuous distribution in the strata above and below the unconformity restricts the precise timing of the corresponding regional intraplate deformation to ca.166–157 Ma and ca.151–129 Ma, respectively, which coincide well with tectono-magmatic events in southern Tibet. Based on previous apatite fission track dating data in Sayan-Siberia orogenic belt and Tianshan-Beishan orogenic belt, we suggest that stages of regional intracontinental deformation in the Junggar Basin and its periphery are related to compressive events on the southern margin of Eurasia. Among them, the first stage of intraplate deformation during ca. 166–157 Ma with shorter duration and slighter intensity may be controlled by the collision of the Karakoram-Lhasa Block with the South Pamir Block and the second during ca.151–129 Ma with longer duration and more intensity may signify the main process of Lhasa and Qiangtang collision and the final full closure of the Bangong-Nujiang Tethys Ocean.