The Devonian subduction-related Heishan mafic-ultramafic intrusion hosting a magmatic Ni-Cu-(PGE) deposit is situated at the southern margin of the Central Asian orogenic belt. The outcrop of the intrusion is ~800 m long and ~470 m wide and dips to the southwest to depths up to 1,300 m. The Heishan intrusion is emplaced in Neoproterozoic dolomitic marble and siliceous slate and dominantly comprises of harzburgite and lherzolite. The stratigraphic reversals of Fo and Ni contents of olivine within the lerzolite and harzburgite indicate injections of several pulses of magmas. The two orebodies (Nos. 1 and 4) within the harzburgite and lherzolite at the lower part of the intrusion host ~35 million metric tons (Mt) of disseminated sulfide mineralization with average grades of 0.6 wt % Ni and 0.3 wt % Cu. The sulfides of the No. 4 orebody are lower in PGE contents on the basis of 100% sulfide (580–1,860 ppb Pt, 720–1,450 ppb Pd, 50–120 ppb Ir) and higher in Cu/Pd ratios (48,000–75,000) relative to the sulfides of the No. 1 orebody and mineralized harzburgites, which have 2,350 to 4,110 ppb Pt, 3,460 to 5,840 ppb Pd, 130 to 160 ppb Ir and Cu/Pd ratios of 16,000 to 26,000. Additionally, the olivines in the No. 1 orebody and mineralized harzburgites have higher forsterite (Fo) and Ni contents than those in the No. 4 orebody. We propose that the sulfide segregation of the No. 4 orebody was associated with extensive introduction of crustal sulfur, which is indicated by high δ34S values (1.9–6.1‰) and low Se/S ratios (230–390 × 10−6). Reworking of early fractionated massive or net-textured sulfides by the new wave of magma containing unfractionated sulfide droplets resulted in the positive correlation between Pd/Ir and Ni/Ir for the disseminated sulfides of the No. 4 orebody. In contrast, low δ34S values (0.43–1.01‰) and restricted range of Pd/Ir ratios indicate that the high PGE contents of the sulfides in the No. 1 orebody and mineralized harzburgites resulted from reaction between the sulfides and new pulses of S-undersaturated magmas. The low PGE grades of the Heishan sulfides indicate that the sulfides were segregated from PGE-depleted parental magmas.