Evolution of the Amsterdam-St. Paul (ASP) plateau is debated as a consequence of the Kerguelen mantle plume interaction with the South-East Indian Ridge (SEIR) or related with a weaker ASP plume origin. We performed an integrated geophysical approach using gravity and magnetic modeling along with the joint inversion of Ps receiver function and Rayleigh wave group velocity dispersion data to determine the crustal architecture, and upper mantle structure below the plateau. The gravity-magnetic model revealed that the plateau is associated with three crustal layers as basaltic layer, gabbroic layer and underplated material underlain by sedimentary strata. Our models further suggests that beneath the ASP plateau the Moho depth varies from ~6.6 to 18.0 km. Joint inversion of Ps receiver function and Rayleigh wave group velocity dispersion curve suggested the Lithosphere-Asthenosphere Boundary at depth of 50 km below the Amsterdam Island. Further seismological result suggests evidence of a Low Velocity Zone below the Moho at depth of 20–36 km which may represent a magma chamber. Our model suggests that the evolution of the ASP plateau is guided by the Amsterdam and St. Paul fracture zones, which acted as a thermal boundary confining the horizontal movement of the ASP plume. We propose that the ASP plateau is not linked with the Kerguelen plume and emphasize origin of the ASP plateau by the interaction of SEIR with the ASP plume.