The Nanmingshui gold deposit, located in the eastern segment of the Kalamaili gold belt (KGB), is hosted by the sub-greenschist facies rocks of the Lower Carboniferous Jiangbasitao Formation. The genesis of this deposit, however, has been debated for decades because of controversial constraints on the P-T-X conditions and origins of hydrothermal fluid and mineralization age. In this study, we present gold-bearing sulfide compositions, fluid inclusions, H-O isotopes, and the results of hydrothermal zircon U-Pb dating to provide new insights into the genesis of the gold deposit. Three gold mineralization stages are recognized: quartz–pyrite–minor native gold veins (early), quartz–tourmaline–arsenopyrite–pyrite–gold–polymetallic sulfide veins (middle), and quartz–calcite veinlets (late). Gold predominantly occurs as native gold with high fineness ranging from 941 to 944 in sulfides and quartz, and some as solid solutions (Au+) within the lattice of pyrite and arsenopyrite. Three types of primary fluid inclusions are identified in hydrothermal quartz: CO2-H2O (C-type), aqueous (W-type), and pure CO2 (PC-type) inclusions. The early-stage quartz mainly contains C-type and minor W-type inclusions, with total homogenization temperatures (Th) of 220–339 °C, salinities of 0.4–3.7 wt.% NaCl eqv., and bulk densities of 0.66–1.01 g/cm3. All three types of inclusions are observed in the middle-stage quartz, of which the C- and W-type inclusions yield Th values of 190–361 °C, with salinities of 0.4–6.0 wt.% NaCl eqv. and bulk densities of 0.69–0.99 g/cm3. The late-stage quartz contains only W-type inclusions that have lower Th values of 172–287 °C, higher salinities of 1.4–6.9 wt.% NaCl eqv., and bulk densities of 0.79–0.95 g/cm3. Trapping pressures estimated from C-type inclusions in the early and middle stages cluster at 280–340 MPa and 220–310 MPa, respectively, corresponding to metallogenic depths of 10–13 km and 8–11 km. The H-O isotopic compositions (δ18Owater = 1.8–10.9‰, δD = −99 to −62.9‰) and microthermometric data indicate that the ore-forming fluids belong to medium–high-temperature, low-salinity, medium-density, and CO2-rich-H2O-NaCl ± CH4 ± N2 systems, probably originating from metamorphic water. Fluid immiscibility is a crucial mechanism for gold precipitation. Additionally, the U-Pb dating of hydrothermal zircons, from the auriferous quartz–tourmaline vein, yield a weighted mean 206Pb/238U age of 314.6 ± 9.6 Ma. Taking all of the above, the Nanmingshui deposit can be reasonably classed as a typical mesozonal orogenic gold deposit in the KGB, which was formed in a Late Carboniferous tectonic transition from syn-collision between the Jiangjunmiao accretionary complex and Yemaquan arc to post-collision in the East Junggar Orogen. Our results serve to better understand the gold mineralization and genesis of the Late Paleozoic orogenic system in the Kalamaili area, Xinjiang.