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We studied the fluid inclusions of the Jiguanshan Mo deposit in China, which is a large porphyry deposit located in the southern Xilamulun Metallogenic Belt. The irregular Mo ore body with various types of hydrothermal veinlets is hosted by Late Jurassic granite porphyry. Intense hydrothermal alterations in the deposit from the core to margin are silicification–potassium feldspar alteration, pyrite–quartz–sericite–fluorite alteration, and propylitic alteration. Based on the mineral assemblages and crosscutting relationships of ore veins, the ore-forming process were divided into three stages and two substages: quartz–pyrite veins (stage I) associated with potassic alteration; quartz–molybdenite–chalcopyrite–pyrite veins (substage II-1) and quartz–molybdenite–fluorite veins (substage II-2) associated with phyllic alteration; and fluorite–quartz–carbonate veins (stage III) with carbonation. Five major fluid inclusions (FIs) types were distinguished in the quartz associated with oxide and sulfide minerals, i.e. polyphase brine (Pb-type), opaque-bearing brine (Ob-type), solid halite (S-type), two-phase aqueous (A-type), and vapor (V-type) inclusions. The FIs of stage I were composed of liquid-rich S-, A-, and V-type FIs with homogenization temperatures and salinities of 490 to 511 °C and 8.9 to 56.0 wt% NaCl equiv., respectively. The FIs of substage II-1 are composed of Pb-, Ob-, S-, A-, and V-type FIs with homogenization temperatures and salinities of 352 to 460 °C and 3.7 to 46.1 wt% NaCl equiv, respectively. The FIs of substage II-2 are Ob-, S-, A-, and V-type FIs with homogenization temperatures and salinities of 234 to 309 °C and 3.7 to 39.2 wt% NaCl equiv, respectively. The FIs of stage III are A-type FIs with homogenization temperatures and salinities of 136 to 172 °C and 1.1 to 8.9 wt% NaCl equiv, respectively. Fluid boiling, which resulted in the precipitation of sulfides, occurred in stages I and II. The initial ore-forming fluids of the Jiguanshan deposit had high temperature, high salinity, and belonged to an F-rich NaCl ± KCl–H2O system. The fluids gradually evolved to low temperature, low salinity, and belonged to a NaCl–H2O system. Studies of the hydrogen and oxygen isotope compositions of quartz (δ18OH2O = − 7.3 to 6.3‰, δDH2O = − 104.3 to − 83.3‰) show that the ore-forming fluids gradually evolved from magmatic water to meteoric water.