The morphostructural characteristics of the main taxa of southern Indian Ocean, such as the Del Cano-Crozet, Conrad, and Kerguelen plateaus, are given based on structural-tectonic analysis. A depth map of the acoustic basement of the eastern part of the Afro-Antarctic megadepression is first built using the digitized NGDS database on the thickness of the sedimentary cover of the Indian Ocean, which is available on the Internet. A critical analysis of deep seismic sounding (DSS) data on the Kerguelen plateu hs been performed. A geochemical analysis of more than 100 samples of basalts, acidic rocks, and rocks of sedimentary origin, collected on the islands of the Kerguelen archipelago and raised by dredging and deep-sea drilling from the Kerguelen and Conrad plateaus, is carried out. The study has shown that the plateaus resemble the Madagascar Ridge in terms of morphostructure and a number of other features. It is concluded that these flat-topped horst massifs were the part of the “structural bridge” that connected Madagascar and the eastern part of mainland Antarctica no later than the Paleogene. A proposed alternative version of the geological interpretation of the deep seismic data states that the plateau has a relatively homogeneous structure along the strike, including a thick (at least 15-km) layer of continental crust. An analysis of the depth map of the acoustic basement made it possible to identify the depocenters of the relatively isolated Enderby, Shackleton and Labuan basins framing the Kerguelen Plateau on the southern side. The paragenetic connections of the Kerguelen Plateau with the basins indicate that the isolation of the Kerguelen Plateau from East Antarctica and the formation of the modern structure of the region began in the Late Cretaceous and ended with the last phase of tectonic activation in the Late Miocene–Pliocene. The results of geochemical analysis show that the geochemical and petrological anomalies of the plateau and islands are associated with the crust, and not with the mantle contamination, as well as with the continental nature of the Kerguelen Plateau.