Magmatic Ni-Cu sulfide deposits in orogenic belts have distinct petrological and geochemical features compared with world-class intraplate magmatic deposits. One such feature is the presence of abundant primary hydrous minerals such as phlogopite and amphibole, indicating a H₂O-rich parental magma. However, the origin and nature of the fluids have not been established. In the southern Central Asian Orogenic Belt, the Permian Baishiquan and Tianyu mafic–ultramafic intrusions host magmatic Ni-Cu sulfide deposits. Both intrusions are composed of lherzolite, olivine websterite, gabbronorite, gabbro, and diorite. The main ore-host rocks are lherzolite and websterite, with disseminated, net-textured, and massive ores comprising the dominant primary ore types. Low zircon ε_Hf (− 6.9 to 7.9 ‰) and varying δ¹⁸O values (5.2 to 6.6 ‰), as well as both arc-type and MOR-type zircon Nb/Yb (0.0013–0.011) and U/Yb (0.33–10.22), identify an altered lower oceanic crust component in the mantle source. A combination of altered lower oceanic crust and upper crust can account for the zircon Hf–O isotopic characteristics. A mixing model further reveals that the Baishiquan and Tianyu magmatic sulfide deposits originated from a depleted mantle source that experienced two stages of subduction metasomatism with a 30% addition of altered oceanic crust in the first stage and 20% in the second. In the second stage, > 10% oceanic sediment with high δ¹⁸O must also have been added to result in olivine δ¹⁸O values higher than those in mantle. This staged evolution is reflected in both the olivine and zircon signatures with olivine from disseminated and net-textured ores at the Tianyu deposit having high δ¹⁸O (4.6 to 6.3 ‰) with a similar range to zircon and high δ⁷Li isotopic compositions (12.03 to 19.46 ‰). Contamination in the source by oceanic sediment with high δ¹⁸O values can account for the olivine δ¹⁸O values (4.8 to 5.7 ‰ at Baishiquan) being higher than those in the mantle, while the addition of brine (5% at the Baishiquan deposit) can explain the olivine δ⁷Li values (20.96 to 31.01 ‰). The results suggest that H₂O content, Li content, and δ⁷Li and δ¹⁸O isotopic signatures in olivine and zircon are good indicators of mantle metasomatism and olivine fluid processes in magmatic Ni-Cu sulfide deposits.