The Neogene deformation of the Kuqa-Tianshan Basin-range System is characterized by discrepancy in paleostress patterns on the basin-range boundary and in the basin interior, and by discrepancy in deformation styles of the basement and the cover. Measurement and paleostress reconstruction of the brittle faults display a stress pattern with NW-SE and/or NNW-SSE extension on the basin margin and NW-SE compression in the basin interior. The basement was cut into blocks separated by boundary faults and upthrusts that were recognized in the seismic reflection profile. The block-faulting could have caused vertical uplift of the basement and gravitational sliding in the overlying sedimentary cover. Theoretical calculation indicates two generations of potential decollement folds within the basin, with one being mudstone in the Triassic Huangshanjie formation and the other the Cenozoic salt-gypsum layers.