Located about 60 km west of the Tuotuohe Town in central Tibet and occurring in the hinterland of Tibetan continent-continent collisional orogen, the Chaqupacha lead-zinc deposit has developed into a major ore deposit in the northern segment of the Sanjiang polymetallic metallogenic belt. In this paper, the authors collated the structures of the ore district on field and microscopic scales, and then analyzed ore-controlling structures. Detailed geological mapping reveals two stages of folding that caused the deformation of the Late Palaeozoic-Early Mesozoic strata, with two Cenozoic thrust nappe systems, i.e., the Tanggula Thrust System (TTS) and the Fenghuoshan-Nangqian Thrust System, superimposed on the folds. Thrust in Chaqupacha has a northward, northwestward, or northeastward dipping plane, dependent on its location, characterized by the thrusting of middle Permian limestone onto late Permian clastic rocks. Miocene Wudaoliang Formation muddy limestone and mudstone occur in the north of Permian limestone, and the strata dip gently or subhorizontally over vast areas, implying that no evident crustal shortening has occurred since Miocene. Field observation and drill data indicate that the contact relationship between Permian and Miocene is unconformity. Besides, normal faults commonly have zigzag geometry in map. These extensional fractures are locally filled with marl of Wudaoliang Formation, where Pb-Zn minerals are well developed. Drilling data reveal that main ore bodies are located at ca. 20 m below the surface and is strictly confined in breccia belts. All Pb-Zn minerals are deposited in open space of the breccia belts, coexistent with marl of Wudaoliang Formation where horizontal stratiform structure is preserved. Such phenomenon suggests that lead-zinc mineralization occurred during the period when the Wudaoliang Formation was deposited.