Direct geological information in Antarctica is limited to ice free regions along the coast, high mountain ranges, or isolated nunataks. Therefore, indirect methods are required to reveal subglacial geology and heterogeneities in crustal properties, which are critical steps toward interpreting geological history. We present a 3D crustal model of density and susceptibility distribution in the Wilkes Subglacial Basin (WSB) and the Transantarctic Mountains (TAM) based on joint inversion of airborne gravity and magnetic data. The applied “variation of information” technique enforces a coupling between inferred susceptibility and density, relating these quantities to the same gravity and magnetic sources to give an enhanced inversion result. Our model reveals a large body located in the interior of the WSB interpreted as a batholithic intrusive structure, as well as a linear dense body at the margin of the Terre Adélie Craton. Density and susceptibility relationships are used to inform the interpretation of petrophysical properties and the reconstruction of the origin of those crustal bodies. The petrophysical relationship indicates that the postulated batholitic intrusion is granitic, but independent from the Granite Harbor Igneous Complex described previously in the TAM area. Emplacement of a large volume of intrusive granites can potentially elevate local geothermal heat flow significantly. Finally, we present a new conceptual tectonic model based on the inversion results, which includes development of a passive continental margin with seaward dipping basalt horizons and magmatic underplating followed by two distinct intrusive events associated with the protracted Ross Orogen.