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The Lower Urgen molybdenum deposit (44,856 t Mo @ 0.141%), situated in the northern Great Xing’an Range, is a newly discovered porphyry molybdenum deposit. Mineralization is characterized by veinlet-disseminated- and vein-type quartz–sulfide orebodies primarily occurring in the cupola of the Early Cretaceous granite porphyry stock. In this study, we present a detailed description of the ore geology, molybdenite Re-Os dating, H-O-S-Pb isotopic compositions, and fluid inclusion (FI) analyses including petrography, laser Raman, and microthermometry to precisely constrain the timing of ore formation, the origin of ore-forming fluids and materials, as well as the metal precipitation mechanism. Molybdenite Re-Os dating yielded two model ages of 141.2 ± 1.5 and 147.7 ± 1.7 Ma, coeval with the regional Late Jurassic–Early Cretaceous molybdenum metallogenesis. The hydrothermal process can be divided into three stages: the quartz–molybdenite(–pyrite) stage, quartz–polymetallic sulfide stage, and quartz–carbonate stage. Four types of FIs were distinguished for quartz, including two-phase liquid-rich (L-type), saline (S-type), CO₂-rich (C1-type), and CO₂-bearing (C2-type) FIs. Microthermometric data showed that the homogenization temperatures and salinities from the early to late stages were 240–430 °C, 5.0–11.9, and 30.1–50.8 wt% NaCl equiv.; 180–280 °C and 3.0–9.1 wt% NaCl equiv.; and 120–220 °C and 0.2–7.9 wt% NaCl equiv., respectively, suggesting a decreasing trend. H-O isotopic compositions indicate that the ore-forming fluids were initially of magmatic origin with the increasing incorporation of meteoric water. S-Pb isotopic compositions indicate that the ore-forming materials originated from granitic magmas, and the mineralization is genetically related to the ore-bearing granite porphyry stock in the deposit. Fluid immiscibility and fluid–rock interaction are collectively responsible for the massive deposition of molybdenite in stage 1, whereas fluid mixing and immiscibility played a critical role in the deposition of polymetallic sulfide in stage 2.