The Bali Basin is located in the Sunda-Banda back-arc from subduction along the Sunda Arc to continental collision along the Banda Arc. Still, its geologic structural patterns have yet to be mapped and discussed in detail as the transition zone. An integrated approach involving magnetic, gravity, and seismic data analysis was undertaken to discover these structures that potentially impact the surrounding area. The magnetic anomalies indicate that the thrust fault structure beneath the north coast of the islands of Bali and Lombok vertically displaces the basement on the seabed. The interpretation, verified with gravity and seismic reflection profiles, indicates a significant, tight, and well-developed expression of blind thrust faulting. Gravity data delineate the basin bedrock surface 6 km beneath the south Bali Basin, where seismic sections show five Cenozoic sedimentary sequences more than 2000 m thick, filling a highly deformed and faulted Cretaceous bedrock sequence. The seismic-gravity model shows sedimentation-related subsidence from basin filling followed by tectonics inversion.