Analyses of bathymetry, gravity and seismic reflection data of the diffusive plate boundary in the central Indian Ocean reveal a new kind of deformed structure besides the well-reported structures of long-wavelength anticlinal basement rises and high-angle reverse faults. The structure (basement trough) has a length of about 150 km and deepens by up to 1 km from its regional trend (northward dipping). The basement trough includes a rise at its center with a height of about 1.5 km. The rise is about 10km wide with rounded upper surface and bounded by vertical faults. A broad free-air gravity low of about 20 m Gal and a local high of 8 m Gal in its center are associated with the identified basement trough and rise structure respectively. Seismic results reveal that the horizontal crustal compression prevailing in the diffusive plate boundary might have formed the basement trough possibly in early Pliocene time. Differential loading stresses have been generated from unequal crust/sediment thickness on lower crustal and upper mantle rocks. A thin semi-ductile serpentinite layer existing near the base of the crust that is interpreted to have been formed at mid-ocean ridge and become part of the lithosphere, may have responded to the downward loading stresses generated by the sediments and crustal rocks to inject the serpentinites into the overlying strata to form a classic diapiric structure.