AbstractDeep crustal seismic reflection profiling is carried out for first time across various tectonic domains of seismically active Mesozoic Kachchh rift basin, formed during the breakup of Gondwanaland. The seismic data, processed using the common reflection surface stack approach, provided maiden images of the shallow and deep sub‐surface structures in the region. These images reveal a 15 km thick subhorizontal lower crustal reflection fabric and crustal‐scale domal‐type structure extending from the surface to the Moho. We interpret the earlier structure represent magmatic underplating and the latter as the Kachchh Mainland uplift. We find large variations in the thickness of sediments from 150 m to 6.5 km and crustal thickness from 45 to 35 km from north to south, with a Moho up warp of 4 km beneath the Kachchh Mainland fault. The Kachchh rift basin exhibits an unusually thick crust of 45 km, contrary to many rift basins. We interpret the syn‐rifting and the Reunion mantle plume activity, manifested as Deccan volcanics, are responsible for magmatic underplating and crustal thickening. Uplift in the region is multi‐genetic in origin. Present study illuminated new faults and nature of various other faults. Moderate to large earthquakes in the region are attributed to the regional and local stresses resulting from the plate boundary and heterogeneous crustal structure. Based on the mafic lower crust and distribution of aftershocks through the entire crust, we interpret the lower crust is brittle, contrary to most models of continental rheology.