The sensitivity of molybdenum (Mo) stable isotopes to redox changes enables innovative geochemical means of tracing the evolution of medium- to high-temperature magmatic hydrothermal processes. However, the Mo isotope geochemical behaviors and fractionation mechanisms in magmatic-hydrothermal systems are still unclear. This study performed high-precision Mo isotope research on well-characterized hydrothermal metal sulfides (pyrite, chalcopyrite, molybdenite and pyrrhotite) from different metallogenic stages and the ore-forming porphyries and surrounding rocks from the giant Pulang porphyry copper deposit in Yunnan, Southwest China, to better understand Mo isotope behaviors in magmatic hydrothermal systems. The results show that compared to the high-temperature magmatic system with homogeneous Mo concentrations (1.44 ppm to 11.3 ppm) and δ98Mo values (−0.41‰ ± 0.05 to −0.08‰ ± 0.03), medium- to high-temperature hydrothermal stage molybdenite displays slightly lighter δ98Mo values (−0.90‰ ± 0.04 to 0.08‰ ± 0.04), and pyrite, chalcopyrite and pyrrhotite, which have low Mo concentrations (0.13 ppm to 28.5 ppm), feature significant δ98Mo variations from −0.34 ± 0.04‰ to 3.01 ± 0.03‰. The absence of fractionated but low δ98Mo values in the magmatic system, combined with the lack of any correlation between the δ98Mo and geochemical index values (e.g., Co/Ni value) of the metal sulfides, implies that the Mo isotope signatures of sulfides in the hydrothermal stage were not inherited from component signatures of the magmatic phase or contamination of surrounding rocks. Our study proposes that heterogeneous partitioning and transportation of heavy/light Mo isotopes into progressively precipitated metal sulfides as a result of changes in the redox-driven metallogenic setting and differential geochemical behaviors of Mo species contribute to the observed δ98Mo variations and that the heavier and strongly variable Mo isotopic signatures correspond to the dominant metallogenic stage of the deposit. Such fractionation may be explained by the Rayleigh fractionation model, whereby 95Mo is preferentially partitioned into isotopically light molybdenite, and the subsequent precipitation of pyrite, chalcopyrite and pyrrhotite from the residual 98Mo-rich ore-forming fluids manifests heavier isotopic compositions. We therefore highlight that the Mo isotopes of metal sulfides provide valuable insights into the precipitation of metal-rich fluids, the identification of favorable mineralization zones, and the ability to trace the evolution of sophisticated magmatic-hydrothermal systems.