The deformation pattern and slip partitioning related to oblique underthrusting of the Tarim Basin in the eastern Tian Shan are not well understood because of the lack of interior deformation images. The Baoertu fault (BF) 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 detailed high-resolution remote sensing image interpretations and field investigations. Three field observation sites along an ~80 km-long fault segment indicate that the BF 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 BF acts as a decoupling zone and accommodates the left-lateral shearing caused by the oblique underthrusting of the Tarim block. In the eastern Tian Shan, 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 at both sides can be viewed as giant positive flower structures.