The Southern Desert (SD) of Iraq is located in the southernmost region of Iraq and is tectonically located on the stable part (proximal domain) of the Arabian Platform. The area is characterized by a considerable thickness of nonmagnetic Phanerozoic sediments overlying a reworked Proterozoic basement. Due to the intense nature of the karst near-surface geology, the basement has neither been seismically imaged nor drilled. In such situations, potential field (gravity and magnetic) exploration methods can often help to identify and map the deep structure of the basement. Here, the aeromagnetic field data, which cover all of the SD, are used to determine the structure and approximate depth of the basement. We use the combined results of the tilt derivative and phase preserving dynamic range compression (PPDRC) methods to qualitatively delineate the main basement structures and then use the source parameter imaging (SPI), tilt-depth (TD), and finite SPI (FSPI) methods to determine the basement depths. The qualitative interpretation of the tilt derivative and PPDRC methods identifies three north–south to northeast–southwest-trending linear negative anomalies that could represent extensional grabens in the basement surface. These grabens divide the basement into three blocks: the northwest block, the central block, and the southeast block. The magnetic anomalies over the basement blocks suggest that the northwest and central blocks are cut by a set of north–south to north-northwest–south-southeast and northeast–southwest faults. Depth estimation methods over the uplifted blocks have minimum depths between 4 and 5 km, whereas, over the graben, the depths range from 7 km to in excess of 12 km. The FSPI method, unlike the SPI and TD methods that use an infinite depth source body, gives depths generally deeper by up to 1.1 km if the assumed Curie-point depth is 21 km. A more realistic Curie-point depth of 32 km is used in the final interpretation model. These inferred basement blocks, grabens, and subbasin structures agree in general with the regional structures associated with the Arabian Peninsula and could provide an important framework for developing future hydrocarbon exploration strategies of the SD.