The quartz porphyries at Yaguila, Tibet, host important polymetallic ore deposits, but their age, source and evolution have received insufficient attention. In this study, LA-ICP-MS U-Pb zircon ages revealed that these quartz porphyries were formed in two stages, i.e. precollisional Early Cretaceous period (ca. 128 Ma) and late subduction to initial collision Palaeogene period (ca. 65 Ma). Geochemical evidence including whole-rock major element, trace element and rare earth element, zircon Hf isotopes together with sulphide Pb isotopes suggests the Early Cretaceous quartz porphyries could have formed by means of partial melting of crustal materials from Lhasa Terrane basement in a thickened crustal tectonic setting, whereas the Palaeogene quartz porphyries by enhanced input of mantle components probably were associated with slab rollback and breakoff at that time. Granitoid magmas produced in this way ascended to upper crustal level and interacted with marbles and breccias to form Pb-Zn-Ag ore bodies and Mo ore bodies, respectively. Age and geochemical constraints on the Early Cretaceous and Palaeogene polymetallic ore bodies not only have favoured a skarn and hydrothermal vein origin over a submarine exhalative sedimentary origin but also have consummated ore deposits metallogenic series and built up a reconnaissance model along the Lhasa Terrane.