The deformation pattern and slip partitioning related to oblique underthrusting of the Tarim Basin in the eastern Tian Shan orogenic belt are not well understood because interior deformation images are lacking. The Baoertu fault is an E-W–striking, ~350-km-long reactivated basement structure within the eastern Tian Shan. In this study, we quantify its late Quaternary activity based on interpretations of detailed high-resolution remote sensing images and field investigations. Three field observation sites along an ~80-km-long fault segment indicate that the Baoertu fault is characterized by sinistral thrust faulting. Based on surveying of the displaced geomorphic surfaces with an unmanned drone and dating of the late Quaternary sediments using radiocarbon and optically stimulated luminescence (OSL) methods, we estimate a late Quaternary left-lateral, strike-slip rate of 1.87 ± 0.29 mm/yr and a N–S shortening rate of 0.26 ± 0.04 mm/yr for this fault. The lithospheric Baoertu fault acts as a decoupling zone and accommodates the left-lateral shearing caused by the oblique underthrusting of the Tarim Basin. In the eastern Tian Shan orogenic belt, the oblique convergence is partitioned into thrust faulting across the entire range and sinistral slip faulting on the high-dip basement structure within the orogen. This active faulting pattern in the eastern Tian Shan of sinistral shearing in the center and thrust faulting on both sides can be viewed as giant, crustal-scale positive flower structures.