The study of extensional fault systems is crucial for deciphering the tectonic evolution of rift basins and revealing regional geodynamic mechanisms. Although physical simulations have demonstrated that stress orientation and basement fault activity are key factors controlling extensional structures, the three-dimensional evolutionary processes of fault systems under the coupled influence of multi-phase extension direction changes and basement fault reactivation remain insufficiently explored. This study employs a physical modeling platform to simulate the evolution of extensional fault systems under two-phase extension with varying directions, based on pre-defined basement faults. During the first-phase orthogonal extension, a fault zone consisting of long straight boundary faults perpendicular to the extension direction and internal short faults was formed, with a transition from soft to hard linkage observed at fault stepovers. In the second-phase oblique extension, pre-existing faults generated during the earlier orthogonal extension continued propagating upward as inherited cover faults, exhibiting a staged evolution: In the initial stage, fault reactivation dominated within the fault zone, characterized by reactivated faults of varying lengths and unchanged strikes; During the intermediate stage, fault strikes within the zone began to shift, accompanied by newly formed faults with heterogeneous orientations, resulting in more complex structural patterns and cross-cutting relationships; In the late stage, an increasing number of peripheral new faults emerged, displaying en-echelon arrangements orthogonal to the extension direction and sensitive to stress field variations. Furthermore, PIV technology precisely captured the spatial reactivation positions of secondary faults and the timing of new fault formation during oblique extension, revealing differential fault development and linkage mechanisms within the fault zone. The experiments demonstrate that the evolution of late-stage fault systems is jointly controlled by basement faults, pre-existing cover faults, and extension direction. Basement faults play a fundamental role in shaping the overall fault zone architecture, while the extension direction significantly influences the morphology and structural characteristics of faults both within and outside the zone. The simulation results align with natural deformation examples, providing a model and guidance for tectonic analysis in similar geological settings.