Abstract The Machangqing porphyry Cu-Au deposit is located in the Sangjiang region, Jinshajiang-Ailaoshan metallogenic belt, southeastern Tibet. It has three main phases of felsic-mafic intrusions: barren granites, ore-forming porphyry intrusions, and mafic lamprophyres. U-Pb zircon dating shows that these intrusions were emplaced over a period of ~3 m.y., with lamprophyres at 36.50 ± 1.6 Ma (1 σ ), porphyry intrusion at 34.26 ± 0.22 Ma (1 σ ), and granite intruded at 34.00 ± 0.26 Ma (1 σ ). The in situ Rb-Sr analysis of phlogopite and amphibole, primary minerals in the lamprophyres, also gives a date of 36.5 ± 1.5 Ma (2 σ ), regarded as the emplacement age of the lamprophyre, earlier than the ore-forming porphyry intrusions. The magmatic phases have significantly different sulfur and chlorine contents. The SO 3 contents of igneous apatite microphenocrysts from the mineralization-related porphyry intrusions are higher (0.24 ± 0.14 wt %, 1 σ , n = 82) than those from the barren granites (0.08 ± 0.07 wt %, 1 σ , n = 30). The chlorine contents in apatite grains from the porphyry intrusions (0.18 ± 0.16 wt %, 1 σ ) are also higher than those from granites (0.04 ± 0.02 wt % Cl, 1 σ ). The apatite in lamprophyres have higher sulfur (0.68 ± 0.19 wt %, 1 σ , n = 40) and chlorine (0.48 ± 0.13 wt %, 1 σ ). The large difference of Cl and S in lamprophyres might suggest that elevated magmatic volatile contents derived from the mafic magma were important for ore formation in the Machangqing porphyry systems. The in situ Sr and O isotopes in apatite phenocrysts from the porphyry intrusions ( 87 Sr/ 86 Sr: 0.70593–0.70850; δ 18 O: 6.0–7.0) are similar to those in the lamprophyres ( 87 Sr/ 86 Sr: 0.70595–0.70964; δ 18 O: 5.4–6.9), consistent with similar origins for their volatile contents. These data may indicate that the deeper magma chamber was recharged by a relatively S-Cl-rich mafic magma similar to the lamprophyres, triggering the ore-forming magmatic event. This study also suggests that origin of apatite Sr and also volatile contents, combined with in situ Sr and O isotopes, could be useful for fingerprinting fertile intrusions associated with mineralization within drainage source areas or in outcrops.