The Naruo porphyry copper deposit containing more than 2 Mt of copper is located in the Duolong ore district in the west of the Bangongco–Nujiang belt in central Tibet. New zircon U-Pb, biotite 40Ar/39Ar, zircon (U-Th)/He ages, published age data together with thermal modeling were presented in this paper to investigate the thermal history of Naruo deposit. Thermal modeling reveals a prolonged magmatic-hydrothermal evolution firstly cooling from ~700°C to ~350°C at 120 Ma, then cooling to 230°C at 106 Ma and maintaining at 200°C from 106 to 90 Ma which is attributed to multiple magmatic events and thermal effect of strike-slip fault. Affected by thrust nappe structure, the sample was consistent with 120°C from 70 to 63 Ma. The Naruo deposit started to experience exhumation at a rate of ~0.07 km/Myr since 60 Ma which is related to India-Asia collision. The prolonged magmatic-hydrothermal evolution process might have important influence on the Naruo deposit. The ore-related intrusions preserved in the foot walls of strike-slip fault and thrust nappe structure are the objects of future exploration in the Duolong ore district.