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 towards interpreting geological history. We present a 3D crustal model of density and susceptibility distribution in the Wilkes Subglacial Basin 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 gravity and magnetic sources to give an enhanced inversion result. Our model reveals a large-scale body located in the interior of the Wilkes Subglacial Basin 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 blocks. The petrophysical relationship indicates that the postulated batholitic intrusion is granitic, but independent from the Granite Harbour Igneous Complex previous described in the TAM area. Emplacement of a large volume of intrusive granites can potentially elevate local geothermal heat flow significantly. Finally, we present a tectonic evolution sketch 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 intrusion events in the Wilkes Subglacial Basin with Pan-African ages (700 - 551 Ma) and Ross ages (550 - 450 Ma).