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The Nezamabad Fault System (NFS) in the Fars area of the Zagros Fold–Thrust Belt represents a persistent, basement-rooted transverse shear zone that fundamentally controls the regional hydrocarbon system. This study integrates seismicity distribution, isopach analysis, and tectono-stratigraphic modeling from the Triassic to the Cenozoic to unravel how recurrent basement reactivation governs trap evolution. Isopach maps reveal a pronounced southwest-thickening asymmetry, with Triassic successions exceeding 1,400 meters, indicating long-term differential subsidence during four key phases: (1) Triassic syn-rift salt accumulation (Dashtak Formation) forming the primary detachment; (2) Jurassic–Early Cretaceous passive subsidence promoting source rock deposition; (3) Mid-Cretaceous transpression enhancing reservoir dolomitization; and (4) Late Cretaceous–Cenozoic inversion generating hybrid traps. Seismicity analysis of over 240 events confirms the 256-km-long NFS is a crustal-scale structure, with most foci at 10–33 km depth and others extending to 150 km, implying lithospheric stress transfer. This deep-crustal activity has periodically reorganized stress, enhanced fracture permeability, and rejuvenated traps through seismic pumping and cross-scale mechanical coupling. The results demonstrate that hydrocarbons in the Fars area are not a passive outcome of folding but a dynamic expression of lithospheric coupling. The findings establish a predictive framework for identifying analogous basement-influenced petroleum systems in other foreland fold–thrust belts worldwide.