The southeastern Brazilian onshore-offshore margin and underlying lithosphere are investigated by three-dimensional magnetotelluric imaging using 202 high-quality broadband and long-period amphibious MT-dataset, orthogonally traversing the regional surface deformation hills of Serra da Mantiqueira and Serra do Mar, as well as the coast-parallel onshore-offshore lineaments. Three-dimensional conductivity model reveals an electrically heterogeneous crust (up to 40 km) in the onshore Brasília and Ribeira Orogenic Belts, and ∼ 2–10 km thick-conductive-sedimentary-wedge beneath the offshore Santos Basin laying on top of a stretched and thinner resistive crust. Regionally, the lithosphere is found ∼130 km thick beneath the most northwestern part of the Brasília Orogenic Belt which is thinning out towards the deep-water Santos Basin (∼70 km). This thinning coincides with the lithosphere-asthenosphere boundary in recent seismic tomography results, reflecting the current state of the uplifted asthenosphere post-West Gondwana break-up. A major steeply dipping sub-lithospheric conductor, in conjunction with a confined asthenosphere upwelling (or lithospheric thinning), has been observed underneath Embu-Paraíba do Sul domain (Ribeira belt), which may be somehow associated with the continental scale rifting, surface uplift and the Cretaceous São Paulo-Rio de Janeiro dykes swarm. Our findings provide valuable insights into the formation of southeast Brazilian highlands and its association with mantle plume-induced lithospheric delamination (or removal) and the occurrence of alkaline magmatism, after reactivation of some pre-existing weak zones.