It is an agreement that collision of Indian and Asian plates causes uplift of the Tibet Plateau. However, great controversy exists about uplifting history and mechanisms of the Tibetan Plateau. Uplift history of the Tibetan Plateau has been well recorded in the Qaidam Basin, located in the northern margin of the Tibet Plateau. In this paper, we recognize and classify faults recorded by subsurface seismic data in the western Qaidam Basin. In addition, we reconstruct the Cenozoic deformation history of the Qaidam Basin based on balanced section of 5 seismic profiles. The results indicates that 1) Faults in the western Qaidam Basin can be classified as growth faults and non-growth faults, and the growth faults could be divided into three subcategories. 2) According to timing and manner of fault activities, faults and strata in the western Qaidam Basin could be divided into two structural layers: the lower (Lulehe Fm-Xia Youshashan Fm) and the upper (Shang Youshashan Fm-Qigequan Fm) layer. 3) The western Qaidam Basin has experienced two intensive tectonic deformations: the first phase occurs at 43.8–22 Ma (Middle Eocene-Early Miocene), which reached peak at 31.5 Ma (Early Oligocene); the second phase occurred between 14.9 and 0 Ma (Middle Miocene-Present), and the second phase is stronger than the first phase. Recognizing early fault activities confirm previous results that northern Tibet has sensed collision between the India and the Asia shortly after the collision. However, our results here emphasize that the northern Tibet has experienced another phase of shortening and uplift in the late Neogene. It was the two-stage tectonic activities that work together to produce the current Tibetan Plateau.