A thrust-fold belt consisting of a series of thrusts and buckling folds developed in the Mesozoic and Cenozoic strata within the Kuqa Depression, Tarim Basin. In this study, a structural interpretation model of the Kuqa Depression is established and the Mesozoic proto-basin is reconstructed on the basis of outcrop geology along the basin margin, seismic, well-log and CEMP data. The model is called ‘delaminate contractional deformation’, which emphasizes the decoupling between the Cenozoic, Mesozoic, pre-Mesozoic and the basin-basement within the Kuqa Depression, but there is no unified detachment. The model has a shortening amount ranging from 12 km to 16 km and the depth involved in contractional deformation ranges from 21 km to 28 km. A prototype of the Mesozoic basin reconstructed by interpretation model is a sub-basin superposed on the transitional zone between the uplift at the northern edge of the Tarim Craton and the southern Tianshan orogenic wedge formed in the Hercynian orogeny. Lithospheric thermal and crustal isostatic activity after the Hercynian orogeny maybe the controlling dynamic factors of basin subsidence during the Mesozoic and early Cenozoic, the difference in rock mechanical properties between different levels, craton and orogenic wedge being the major cause of the ‘delaminate contractional deformation’ during the Himalayan orogeny.