The supergiant Shizhuyuan W–Sn–Mo–Bi polymetallic deposit is located in the Nanling Range, and is intimately related to the Qianlishan granite complex intruded during the Late Jurassic period. The complex consists of three intrusive phases: porphyritic biotite granite (PBG), equigranular biotite granite (EBG), and porphyritic granite dyke. In this work, the distinct geochemical features of magmatic and hydrothermally-altered zircons from the Qianlishan complex are used to reveal the magmatic-hydrothermal evolution of the deposit. Whole-rock geochemistry and mineralogy show that EBG samples have experienced stronger fractional crystallization than PBG samples. Zircon U–Pb dating constrains the intrusive episodes at 155–153 Ma and ~152 Ma for the PBG and EBG, respectively, and subsequent hydrothermal events (revealed by hydrothermal zircon ages) at 154–153 Ma and 152–150 Ma. Hydrothermally-altered zircon and paragenetic mineral inclusions from EBG samples show textures and compositional properties suggesting they were intensely altered by a zirconium saturated aqueous fluid (Type 1), enriched in most trace and metallogenic elements (e.g., Zr, REEs, Hf, P, U, Th, Nb, Ta, Ti, Pb, Al, Fe, Mg, Ca, Mn, W, and Sn) and volatiles (F, Cl, Li, CO2 and H2O). This fluid was relatively lower in temperature, pressure and oxygen fugacity (average Ce4+/Ce3+ = 11.2). Type 2 fluid, represented by hydrothermally-altered zircons found in PBG, was depleted in trace elements and had a relatively higher temperature and pressure and low fO2 (Ce4+/Ce3+ = 2.12–29.16). Type 3 fluid, as evidenced by fluid-altered zircons from the greisenized granite, was likely a further evolved product of the Type 2 fluid, given its moderate cargo of most trace elements but also with exceedingly low Ce4+/Ce3+ values (2.9–33.45). The Type 3 fluids might be precursors of W–Sn mineralizing fluids, whereas the Type 1 fluids were likely to represent mature ore-forming fluids, which were activated during the late skarn stage but before the retrograde mineralization stage. Compared with the fO2 of PBG and EBG magmas calculated by non-altered magmatic zircons (average Ce4+/Ce3+ = 31.47 and 49.21), it seems that the hydrothermal fluids generated by them became more reduced during the further evolution. A progressive process can thus be divided: PBG → Type 2 → Type 3 → EBG → Type 1, with the gradual accumulation of ore-forming materials. The enrichment of most elements in hydrothermal zircons further indicates a substitution of Y, REEs, P, Hf, U, Th, Ti, Nb, Ta, Ca, K, Fe, and Mn for Zr4+ and Si4+ in the zircon lattice. Most fluid-altered zircons exhibit a similar 176Hf/177Hf distribution range (−11 to −6) but evidently elevated 176Lu/177Hf and 176Yb/177Hf ratios with magmatic ones. This indicates that three types of hydrothermal fluids were magmatic-derived, whereas Lu and Yb were highly mobile during the hydrothermal event. Based on the results, a magmatic-hydrothermal evolution model is presented for Shizhuyuan zircons. This research highlights the use of zircon as a powerful tool in revealing the complex magmatic-hydrothermal processes and perhaps mineralization potential in (highly evolved) granite-associated mineralization systems.