The Bailongshan Pegmatite deposit, located in the West Kunlun Orogenic Belt, Northwest China, is a newly discovered, super-large Li–Rb (Be–Ta–Nb) rare-metal deposit. Since complex magmatic-hydrothermal processes are responsible for the mineralization of such rare-element pegmatites, it is desirable to study the evolution and sources of ore-forming fluids to analyze the genesis of ore deposits. In this study, the 40Ar/39Ar plateau ages of muscovite and biotite were determined to be 171.36 ± 1.87 and 172.39 ± 1.66 Ma, respectively, indicating that the duration of hydrothermal mineralization was approximately 170 Ma. Based on the zonal nature of the mineral assemblage, the Bailongshan area was divided into four zones and stages (I–IV), namely the albite–quartz–lithium tourmaline (AQT, stage I), albite–quartz-bearing mica (AQM, stage II), albite–quartz–spodumene (AQS, stage Ⅲ), and spodumene–quartz (SQ, stage IV) zones. Among these, AQS and SQ were the main ore-bearing areas. In terms of the fluid inclusions found in quartz and spodumene, the different types include a gas-rich phase (V-type), a liquid-rich phase (L-type), a daughter mineral-bearing three-phase (S-type), and a carbon dioxide-bearing phase (C-type). In stage I, the homogeneous temperatures of the V- and S-type fluid inclusions varied from 365 to 415 °C, while their corresponding salinities were 8.5–12.9 and 44.8–47.2 wt% NaCl equiv., respectively. In stage II, the homogeneous temperature and salinity of the L-type inclusions were 315–365 °C and 9.9–13.3 wt% NaCl equiv., respectively, while in stages Ⅲ and IV, the homogeneous temperatures of the L- and S-type fluid inclusions were between 235 and 335 °C, while their salinities were 7.2–12.3 and 32.1–37.0 wt% NaCl equiv., respectively. Furthermore, for the C-type inclusions, the homogeneous temperature and salinity were 235–320 °C and 4.9–10.6 wt% NaCl equiv., respectively. The laser Raman results showed that the fluid in the metallogenic stage was an H2O–NaCl–CO2–CH4 system. Based on the homogeneous temperature and salinity results, the fluid capture pressure from stage III to stage IV was calculated to be 280–150 MPa, and the depth of the capture was >6 km. Moreover, the H–O isotope results suggested that the early ore-forming fluids are mainly magmatic hydrothermal fluids, whereas the later (stage IV) mineralizing fluids may be mixed with a small amount of meteoric water. The subsequent immiscibility of the fluid may be one of the factors responsible for the discharge and precipitation of minerals.