The basement surface and sediments of the Kochkor basin have been studied by structural geological and geophysical methods. The work included high-resolution mapping of the southern basin margin, with a focus on Cenozoic basin stratigraphy, structural unconformities, basement/sediment contacts, and latest deformation (folds, fractures, and faults). Magnetotelluric (MT) soundings provided insights into basin and basement structure, especially important in the poorly exposed eastern flank of the basin margin. The sections across the southern margin of the basin based on geological and geophysical data reveal deformation in both the basement and the sediments. Deformation in sediments shows up as folding, conformal peneplain surfaces, large faults, low-angle detachment faults, and related thrust-fold belts. Thrusting in sediments is inferred to result from cataclastic flow and mass redistribution in disintegrated basement granites. With this mechanism, the total amount of thrusting in the central part of the basin can exceed the convergence of the basin sides.