We present a detailed structural analysis of geometry and temporal development of the Cenozoic faults in the southwestern part of the Qaidam Basin—the largest petroliferous sedimentary basin and the only one producing oil and gas within the Tibetan Plateau, northwest China—based on three-dimensional (3D) seismic and well-log data. The Cenozoic faults are mostly steep (50–70°), basement-involved reverse faults trending primarily west-northwest and secondarily north–south. The two fault sets are commonly linked to each other by west-northwest-oriented faults bending either southward at their eastern tips or northward at the western tips, and originated possibly from inversion of pre-existing extensional faults in response to the far-field effect of the Cenozoic India–Eurasia collision. Faults or fault segments active during different time periods were identified from isopach maps and verified via seismic reflection profiles, showing that the faults became active as early as the Paleocene in the southern part of the southwest Qaidam Basin and propagated dominantly northward and subordinately eastward over time. Measurement of throws on major faults indicates that fault activity intensified over time and culminated since the mid-Miocene. These faults have been an important factor in forming the oil fields in the southwest Qaidam Basin by improving permeability, forming anticlinal traps, and acting as conduits for oil migrating from source rocks to the reservoirs.