The Ross Ice Shelf (RIS) has long obscured the structure of the extended crust of the southern Ross Embayment. Here, we use airborne magnetics data from the ROSETTA-Ice project to estimate the depth to crystalline basement and sediment thickness beneath the RIS. We estimate the depth to the top of the magnetic crust, using a Werner deconvolution in a 2-D moving window applied to aeromagnetic data at 10 km line spacing. The result is then filtered, clustered, and gridded solutions to achieve a continuous basement surface. This method was tuned with seismic acoustic basement in the Ross Sea and magnetic basement determined from Operation Ice Bridge flight line data over both the Ross Sea and the RIS. Sub-RIS sediment thickness was then calculated relative to bathymetry. Shallow basement and thin sediments beneath the RIS define two major basement highs. A throughgoing, wide basement high is located midway across the RIS, and appears to form a southward continuation of the Ross Sea’s Central High. The other prominent basement feature underlies Roosevelt Island, with a continuation SE to the grounding zone. An elongate basin between the two highs deepens southward, reaching its greatest depth beneath Siple Dome. A deep oval basin flanks Crary Ice Rise. Both basins contain >2 km sediment. Bordering the Transantarctic Mountains (TAM) there is a deeper and broader basement basin that contains a narrow, linear, NW trending basement ridge. The magnetic basement is shallower toward Marie Byrd Land and deeper near the TAM/East Antarctica, consistent with contrasts in magnetic and gravity signatures of the crust on either side of the mid-RIS high. The trend of basement highs and basins parallel to the central TAM front suggests that the basement relief ≥2 km is structurally controlled, and is a product of regional extension. Basin sediments may be a source of deformable subglacial bed conditions for grounded ice, and basin flanking faults may control geothermal flux and subglacial water transport. These considerations have a bearing on sub-RIS boundary conditions that are important for cryosphere-ocean numerical modelling frameworks. Our work extends the current knowledge of sub-RIS sediment distribution, continental rifting orientations and the likely locations of basin flanking faults.