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The Beiya porphyry‐skarn Au deposit is one of the largest gold deposits in China, temporally and spatially associated with Eocene intrusions in a post‐collisional setting in western Yunnan, China. In this study, we report new whole‐rock geochemistry, Sr‐Nd isotope, zircon U‐Pb geochronology and in situ zircon Hf‐O isotopes of quartz‐monzonite and biotite‐monzonite porphyries from the Beiya deposit. The porphyry‐skarn mineralization at the Beiya deposit is mainly associated with the quartz monzonite porphyry (35.8 ± 0.6 Ma), while the biotite‐monzonite porphyry (34.3 ± 0.5 Ma) represents a post‐mineralization intrusion crosscutting the main orebodies and the quartz‐monzonite porphyry. Both intrusions have high‐K and adakitic composition and are characterized by high Sr/Y ratios, high SiO2 and Al2O3 concentrations (SiO2 = 69.80–73.86 wt%; Al2O3 = 14.11–15.19 wt%), and low MgO, Cr, and Ni concentrations (MgO = 0.2–1.0 wt%; Cr = 1.76–11.13 ppm; Ni = 2.52–11.72 ppm). Their Sr‐Nd isotope compositions (87Sr/86Sr = 0.7066–0.7077; εNd(t) = –5.3 to –1.5) are consistent with the lower crustal‐derived amphibolite xenoliths (87Sr/86Sr = 0.7060–0.7100; εNd(t) = –10.0 to 0.0), indicating that they might be derived from a thickened juvenile lower crust beneath the Yangtze Craton. The biotite‐monzonite porphyry has lower zircon δ18O values of +5.3‰ to +6.8‰ and higher εHf(t) values of –2.3 to +5.5 than those of the quartz‐monzonite porphyry with δ18O values of +7.1‰ to +8.2‰ and εHf(t) values of –3.8 to +1.5, implying that they were derived from different parts of the lower crust. High Ba/La and Pb/Ce ratios suggest that the quartz‐monzonite porphyry is derived from a volatiles‐rich reservoir. Relatively higher La/Yb, Sm/Yb and Dy/Yb ratios of the biotite‐monzonite porphyry indicate residual garnet in the source, indicating a deeper source than that of the quartz‐monzonite porphyry. The hydrous components should be represented by the amphibole‐rich lithologies, which has relatively shallower depth than that of the garnet‐bearing mafic thickened lower crust. Our data suggest that the mineralized quartz‐monzonite porphyry at the Beiya deposit is derived from partial melting of amphibole‐rich lithologies in the upper part of the thickened juvenile lower crust beneath the Yangtze Craton, while the post‐mineralization biotite‐monzonite porphyry is derived from the basal, and volatiles‐poor, part of the juvenile lower crust. [ABSTRACT FROM AUTHOR]