The origin of the Exmouth and Dampier Sub-basins in the inner rift system of the North West Shelf, Australia, remain poorly understood, despite intensive industrial exploration for more than 50 yr. By integrating deep two-dimensional and basinwide three-dimensional seismic reflection data, it is concluded that the Exmouth and Dampier Sub-basins are primarily controlled by crustal-scale faults that separate different crustal entities of the Pilbara craton/Capricorn orogen and the Exmouth Plateau. These faults were first formed during late Paleozoic rifting and were reactivated during Late Triassic to Late Jurassic rifting. The reactivation of these faults was accommodated by monocline deformation in the stratigraphic cover due to the presence of thick (∼7 km), mechanically weak layers of upper Paleozoic and Lower to Middle Triassic units. The monocline is connected by a ramp syncline that constitutes the main part of the depocenters of the Exmouth and Dampier Sub-basins. It was partially breached by the Rankin fault, a northeast-trending, right-stepping fault system, during Callovian–Oxfordian extension and controlled the development of crestal-collapse grabens in the hanging wall. This study reveals crustal-scale, extensional fault-related folds and their complexity in secondary structures in unprecedented detail. It provides a guideline for understanding extensional fault-related folding in three dimensions and deep petroleum system exploration in other extensional basins worldwide.