The Huangshui’an deposit located in East Qinling (China) is an unusual case of a Si-rich carbonatite hosting economic Mo and minor Pb and REE mineralization. The role of mantle-sourced carbonatite melts and fluids in the formation of the Mo mineralization remains poorly understood. Our integrated study based on field geology, petrography, microthermometry, and LA-ICP-MS analysis of single fluid inclusions, and noble gas isotopes of pyrite permits to reconstruct the source characteristics, the magmatic-hydrothermal evolution of the carbonatitic fluids, and their controls on Mo mineralization. Fluid inclusions hosted in calcite in the carbonatite dikes have the highest concentrations of Mo (9.9–62 ppm), Ce (820–9700 ppm), Pb (1800–19500 ppm), and Zn (570–5800 ppm) and represent the least modified hydrothermal fluid derived from the carbonatite melt. Fluid inclusions hosted in calcite (Cal) and quartz (Qz2 and Qz3) of the stage I carbonatite dikes have different metal concentrations, suggesting that they formed from two distinct end member fluids. The FIA in calcite represent fluid A evolved from carbonatite melt with relatively high-ore metal concentrations, and those in quartz characterize fluid B having a crustal signature due to metasomatic reactions with the wall rocks. The FIA in quartz (Qz1) within the altered wall rock have overlapping elemental concentrations with those of massive quartz (Qz2) and vuggy quartz (Qz3) in carbonatite. This suggests that the volumetrically significant quartz in the Huangshui’an carbonatite has been formed by the introduction of Si by fluid B. The positive correlations between Rb, B, Al, Cl, and Sr in stage II fluid inclusions in late fluorite + quartz + calcite veins indicate that this late mineralization formed from the mixing of primary hydrothermal fluid B with meteoric water. The He–Ar isotope data, in combination with available C–O–Sr–Nd–Pb isotope data, constrain the carbonatite source as an enriched mantle source modified by contributions from crustal material which was probably the fertile lower crust in the region. This distinct source facilitated the enrichment in Mo, REE, and Pb in the primary carbonatite magma. The carbonatite magmatism and Mo mineralization at 209.5–207 Ma occurred in the regional-scale extensional setting at the postcollision stage of the Qinling Orogenic Belt.