Fluorite is a widespread mineral in porphyry and hydrothermal vein Mo-polymetallic deposits. Here, fluorite is utilised as a probe to trace the fluid source and reveal the fluid evolution process in the Chalukou giant Mo (Pb–Zn) deposit, Northeast China, which is characterised as early porphyry Mo and later vein-style Zn–Pb mineralisation. A detailed rare earth element (REE) and Sr–Nd isotope study of fluorite combined with Sr isotopes of sphalerite is conducted for the Chalukou deposit. The chondrite-normalised REE patterns of fluorites from molybdenite veins show light REE (LREE)-enriched patterns, with negative Eu anomalies (δEu = 0.60) and weakly negative Y anomalies (Y/Y* = 0.72). The fluorites associated with sphalerite veins exhibit rare earth element (REE)-flat patterns with negative Eu anomalies (δEu = 0.65 to 0.99) and positive Y anomalies (Y/Y* = 1.37 to 3.08). In addition, during the progression from Mo to Zn–Pb mineralisation, the total concentration of REEs decreases from 839 ppm to 53.7 ppm, and Y/Ho ratios increase from 22.1 to 92.5. These features may be explained by the different mobilities of REE complexes during fluid migration. The Eu anomalies are considered to be inherited from source fluids. All the initial 87Sr/86Sr ratios of fluorite and sphalerite are between those of ore-forming porphyries and wall rocks (rhyolite), with fluorite ratios ranging from 0.706942 to 0.707386 and sphalerite ratios varying from 0.705221 to 0.710417. The majority of εNd(t) values of fluorite varying from −6.4 to −3.6 are also located between the ratios exhibited by ore-forming porphyries and rhyolite, whereas three εNd(t) values of fluorites ranging from −0.26 to 0.36 are close to those of ore-forming porphyries. All the isotopic features indicate that the Sr-Nd isotope ratios of hydrothermal fluid are derived from porphyries and disturbed by fluid–rock reactions. Together with a two-stage Sr–Nd isotope mixing model, we suggest that different sources and fluid–rock interactions (syn-ore intrusions and strata) finally influence the Sr–Nd isotopes of the ore-forming fluids, which are recorded by the majority of fluorite and sphalerite.