In the Eocene Upper Xiaganchaigou Formation from depths of about 3.6–4.9 km in the Shizigou (SZG) Structure in the SW Qaidam basin, core and image logs reveal three fracture assemblages (A-C) comprising opening-mode fractures and faults. Assemblages are defined by structural style (groups of fracture types), and orientation patterns and thus kinematics and separated by relative timing by the unlithified rock style of deformation of assemblage A and fracture crosscutting relations between assemblages B and C. Correlation of fracture kinematics with the structural history of the basin suggests a multi-stage fracture population in the Shizigou Structure arising as a response to Eocene transtension, Miocene transpression, and Quaternary shortening under the influence of the Cenozoic evolution of two boundary faults, the Altyn Tagh Fault (ATF) and the Qimen Tagh-Eastern Kunlun Fault (QTEKF). To clarify the relation, we document formation process of multi-stage fractures in cores and their preferred orientations in log images in five wells. Using image logs from horizontal wells (Shi A and B) at ca. 3.7–3.9 km depth and statistical methods for quantifying spatial arrangement patterns, we identified statistically significant conductive fracture clusters; opening-mode fractures of the assemblage B are significantly hierarchically clustered. Combining fracture mode and their preferred orientations with reconstructed stress history, we propose that the deformation history of the fracture population is kinematically related to the Cenozoic activity of the ATF and the QTEKF. The initial stage of fracture formation is associated with Eocene strike-slip faulting along the ATF, followed by the Early Miocene initial transpressional faulting along the QTEKF and finally intensified shortening since the Quaternary, respectively.