The Early Cretaceous and Paleogene rift structures of the Shanan and Chengbei sags were inherited from basement tectonic deformation of Indosinian and Yanshanian tectonism. However, the architecture of the basement structures and its influence on the structural configuration of later rift development are poorly understood, which impeded hydrocarbon exploration efforts in the study area. Based on 2D high-resolution seismic reflection data in the study area and onshore field data in the Luxi area, we recognize the Indosinian NW-striking low-angle fold-thrust belts and Yanshanian NE-striking high-angle thrusts in basement of the study area. The pre-rift NW- and NE-striking basement structures exert a crucial influence on the two-phase rift architecture and structural evolution of the study area: (1) Low-angle NW-striking Indosinian thrusts are dominantly reactivated as dip-slip major normal faults during Early Cretaceous, such as the Shanan fault and Chengbei faults. The high-angle Yanshanian NE-striking thrusts are primarily reactivated as left-lateral strike-slip faults during this stage, such as the Shaxi fault. (2) During the Paleogene, oblique extension took place across the pre-existing NW-striking reactivated normal faults. A set of half-grabens formed along the major NW-striking oblique-slip faults and large amount of ENE-striking secondary normal faults developed in the NW-striking sags. The pre-existing left-lateral NNE-striking faults shifted to become right-lateral and extensional faults. The Early Cretaceous rift was primarily controlled by NE-SW-directed extension, which was derived from the large-scale left-lateral strike-slip movement of the Tan-Lu Fault Zone. The Paleogene oblique rift was induced by NNW-SSE-directed extension related to the upwelling water-rich mantle wedge of the Pacific subduction zone.