The orogenic gold deposits along the NNW-trending Ailaoshan shear zone are formed during Miocene continental collision, after a complex history of Neoproterozoic subduction, Late Triassic amalgamation between the Indochina and South China blocks after closure of the Paleo-Tethyan Ocean, and Oligocene-Eocene continental-scale shearing related to the Indian-Eurasian continental collision. As a result, the eastern Neoproterozoic basement with ductile shear zones was thrust over the western metasedimentary rocks and Paleo-Tethyan ophiolites affected by brittle faulting. These tectonically juxtaposed successions were underlain by lithosphere metasomatized in the Neoproterozoic. The gold-hosting western succession is characterized by tightly folded Silurian to Permian metasedimentary rocks, overlain by gently folded Late Triassic metasedimentary rocks, and cut by secondary NW-trending shear zones. This crustal architecture controlled migration of ore fluid towards the cessation of regional ductile deformation at ca. 22 Ma, with major ductile shear zones serving as the main conduit, tight folds, and jogs or intersections on subsidiary brittle shear zones as the fluid trap, and Late Triassic rocks as the seal. Gold-rich rims on disseminated gold-poor sedimentary pyrite with a limited δ34S range from − 3 to 3‰, pyrite He-Ar isotope ratios, and the timing of mineralization within retrograde metamorphism suggest an important metal contribution from mantle lithosphere. The auriferous fluid, derived from previously metasomatized mantle lithosphere, is interpreted to have advected up the Ailaoshan shear zone into the metasedimentary sequence during mantle upwelling, clearly contrasting with widely accepted crustal metamorphic models for Phanerozoic orogenic gold deposits.