The Zhubu mafic-ultramafic intrusion of the Permian Emeishan large igneous province (LIP), SW China hosts a magmatic Ni, Cu and platinum-group element (PGE) deposit. It consists of a layered sequence with sub-horizontal modal layering wrapped by a sub-vertical marginal zone. Our new zircon U-Pb isotopic dating gives a mean age of 263.2 ± 5.6 Ma for the layered sequence. The volatiles extracted from the mineral separates of the Zhubu intrusion are composed of predominant H2O (11,769.84 mm3 ·STP/g, STP-standard temperature and pressure) and minor H2 and CO2. The layered sequence has lower H2O but higher H2, CO2, H2S and SO2 contents than the marginal zone. The CO2 and CH4 extracted at 400–900 °C and 900–1200 °C have light δ13CCO2 varying from − 17.45‰ to −7.10‰ and δ13CCH4 varying from −41.35‰ to −22.88‰. The pyroxene separates have significantly lower (87Sr/86Sr)i values (0.705882 to 0.708912) and slightly higher εNd (t = 263 Ma) values (−2.8 to 0.7) than the whole rocks. The εHf (t = 263 Ma) values of zircon crystals vary from −3.05 to +1.90. The chemical compositions of volatiles from the Zhubu intrusion indicate a slightly reduced condition and a H2O-rich parental magma. The C-Hf-Sr-Nd isotopes for the Zhubu intrusion are consistent with ~15 wt% assimilation of the upper crust by a mantle-derived magma. The carbon isotopes indicate that a thermogenic component from sedimentary organic materials was present in the contaminated magma. A weak positive correlation between volatile and PGE contents, together with the C-Hf-Sr-Nd isotopes, indicates that sulfide saturation in the Zhubu magma was triggered by crustal contamination including the addition of volatiles.