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The northeastern periphery of the Qaidam Basin is a crucial region for comprehending the northeastward growth of the Tibetan Plateau, as it documents Late Cenozoic crustal deformation that elucidates the plateau's growth process. In this study, we reconstruct three stages of crustal deformation in the northeastern periphery of the Qaidam Basin during the Late Cenozoic based on interpretation of growth strata from five seismic profiles, structural mapping of the typical superimposed folds and detailed detrital zircon analysis within the study area. (1) During the Early Miocene to Late Miocene period (23–8.6 Ma), there was NW–SE extensional deformation in the northeast margin of the Qaidam Basin, which exerted control over the deposition of the Youshashan Formation. (2) The NW–SE shortening occurred during the Late Miocene period (8.6–8.1 Ma), subsequent to the deposition of the Youshashan Formation and preceding the deposition of the Shizigou Formation, resulting in a parallel unconformity between these two geological units. (3) The intense shortening of the NE–SW direction occurred during the Late Miocene and Pliocene epochs (8.1–2.5 Ma). The timing of this deformation aligns with the sedimentary age of the Shizigou Formation, suggesting that the initial deformation age may represent the onset of NE extrusion from the Tibetan Plateau towards the northeast margin of the Qaidam Basin. The present study not only delineates a Late Cenozoic structural dome resulting from two‐stage crustal shortening in the northeastern periphery of the Tibetan Plateau, but also provides a crucial evidence for reconstructing the Late Cenozoic intracontinental deformation process in this region. [ABSTRACT FROM AUTHOR]