The paper considers geological and geophysical data on the crustal structure of the volcanic Kerguelen Plateau and nearby Indian Ocean, as well as evolution of the Kerguelen Plateau during the Gondwana breakup. It is assumed that three isolated continental blocks (microcontinents) evolved within the Kerguelen Plateau. In order to provide insight into the mechanisms for the microcontinent formation, physical modeling under three different conditions has been carried out. The first experiment simulates a homogeneous lithosphere with two rift fractures propagating toward each one other; in the second experiment, the propagating rift fractures collide with a structural barrier having a stronger lithosphere; the third experiment simulated the effect of a local heat source (a hot spot). Based on these experiments and taking into account the available structural and geophysical data, it is suggested that isolation of continental block in the southern Kerguelen Plateau could have begun due to counterpropagation of rifting branches: oceanic from east to west and continental from west to east. The isolation of the southern block with attachment to the Antarctic Plate took place 120 Ma ago after extinction of the spreading ridge in the Princess Elizabeth Trough. Because of the structural inhomogeneity in the prebreakup lithosphere, which is represented by a zone of intracontinental Lambert-Mahanadi rifts, opening of the ocean could have developed in a more complex regime. Under the effect of a hot spot, a jump of the spreading axis occurred at the moment of its emplacement into the lithosphere.