Sn-polymetallic deposits in the Southern Great Xing’an Range (SGXR) are typically marked by the coexistence of Sn, Cu, Pb, Zn, and Ag, yet the mechanisms controlling their paragenesis and separation remain poorly constrained. The Hujiadian deposit hosts Sn, Cu, Pb, Zn, and Ag mineralization that occurs both as intergrown assemblages within individual orebodies and as distinct but spatially associated orebodies, making it an ideal natural laboratory to investigate element coexistence and fractionation. Three hydrothermal stages are identified: pyrite + cassiterite ± chalcopyrite + quartz + chlorite (Stage I); chalcopyrite + sphalerite ± galena + quartz + fluorite + chlorite ± amphibole ± epidote (Stage II); and sphalerite + galena + pyrite + quartz + chlorite + calcite (Stage III). The rhyolite porphyry yields a zircon U–Pb age of 132.3 ± 2.4 Ma, whereas the Sn ores yield cassiterite U–Pb ages of 129.9 ± 1.3 to 131.4 ± 0.8 Ma. These overlapping ages, within analytical uncertainties, constrain the Sn mineralization to the Early Cretaceous. The rhyolite porphyry is geochemically characterized by a peraluminous, high-K calc-alkaline affinity, coupled with elevated SiO₂ and alkali contents, strong negative Eu anomalies, and low fO₂ (ΔFMQ = −4.9 to 1.1). Collectively, these features are consistent with extensive fractionation under reducing conditions, which would have facilitated Sn accumulation in the residual melt. Pervasive chlorite in the deposit records the physicochemical evolution of the hydrothermal system; four chlorite generations document a shift from early acidic conditions during Sn mineralization to near-neutral or weakly alkaline conditions during late Pb–Zn precipitation. We propose that increasing pH played an important role in promoting cassiterite precipitation during Stage I, whereas cooling was the dominant control on Cu precipitation during Stage II. During Stage III, further cooling and increasing pH promoted Pb–Zn precipitation. The observed carbonatization and mineral assemblages are consistent with possible involvement of external fluids, including meteoric water. These changes may have been associated with fluid–rock interaction and possible mixing with meteoric water.