The Zhunuo porphyry copper deposit in the Gangdese belt of southern Tibet contains 2.37 Mt at 0.57% Cu. In this deposit, Eocene rhyolite (51.6 ± 1.0 Ma) and quartz porphyry (49.1 ± 0.6 Ma) were intruded by monzogranite (14.7 ± 0.3 Ma) and monzogranite porphyry (14.5 ± 0.2 Ma) which commonly host mafic microgranular enclaves (14.9 ± 0.3 Ma). Late-mineralization diorite porphyry (14.2 ± 0.2 Ma) and post-mineralization lamprophyre dikes (12.2 ± 0.1 Ma) and granite porphyry (12.0 ± 0.2 Ma) crosscut the Miocene intrusions. Two quartz–molybdenittie veins yielded molybdenite Re-Os model ages of 14.8 ± 0.1 Ma and 14.4 ± 0.1 Ma, and another two quartz–muscovite–llite–pyrite–molybdenite veins yielded molybdenite Re-Os model ages of 14.2 ± 0.1 Ma and 13.5 ± 0.1 Ma. Zhunuo is characterized by early potassic alteration and associated quartz A veins centered on the monzogranite porphyry and adjacent monzogranite, distal propylitic alteration in the rhyolite, and late-stage phyllic alteration and associated quartz B veins, followed by D veins that affected quartz porphyry and potassic-altered rocks. Copper ores are mainly distributed in the potassic alteration zone that was overprinted by phyllic alteration. Copper mineralization likely occurred during potassic alteration stage and was locally remobilized and redeposited during phyllic alteration stage, or occurred during phyllic alteration stage. The post-mineralization granite porphyry has lower whole-rock Sr/Y (< 20) and εNd(t) (− 9.3 to − 9.0) and higher zircon U/Yb (4 to 27) than the Miocene intrusions (Sr/Y > 40; εNd(t) = − 6.9 to − 6.1; U/Yb = 1 to 10). Limited input of juvenile melts could explain the low potential for copper mineralization in the post-mineralization granite porphyry at Zhunuo.