Numerous early Paleozoic mafic–ultramafic intrusions that host important Ni-Cu sulfide mineralization occur in the northern part of the Qinghai-Tibet Plateau, NW China. The sulfide-bearing Shitoukengde Ni-Cu deposit, which is hosted in a ∼424 Ma mafic–ultramafic intrusion, is one of the most represent magmatic sulfide deposits in the East Kunlun Orogenic Belt. The intrusion is composed of a large gabbroic body, cut by lherzolite, olivine websterite, websterite, and minor dunite. Disseminated and net-textured sulfide mineralization occurs as lenses in the center and towards the bottom of the ultramafic bodies. The sulfide mineralization has variable sulfur contents of 0.3 to 13.6 wt% with Ni grade of 0.41 wt% on average, and low platinum-group element (PGE) concentrations (<8.2 ppb Ru and <11.9 ppb Pd). Pd and Ru tenors of bulk sulfides in the deposit are characterized by a positive correlation, indicating that PGE tenor variations are mainly controlled by varying R-factors (magma/sulfide mass ratio). The estimated PGE concentrations in the Shitoukengde magma are about three orders of magnitude lower than those in continental tholeiites. The significant PGE depletions in the Shitoukengde deposit may be due to sulfide removal in the magma conduit at depth. Our new sulfur isotope data reported range in δ34S values from −5.0 to 4.9‰ for the sulfide minerals of the Shitoukengde deposit, clearly distinct from those of mantle-derived sulfur (0 ± 2‰) and immediate country rocks (1.1 to 2.0‰). This, together with the modeling for S isotope variation as a function of R-factor, suggest that the current δ34S range is attributed to the addition of external sulfides with anomalous δ34S into the magma at depth, followed by progressive modification to crustal signature by uncontaminated pulses of magma. The ultramafic rocks exhibit low εNd(t) values (−4.71 to 2.12) and high (87Sr/86Sr)i ratios (0.7073 to 0.7130), which are more enriched relative to the isotopic compositions of depleted mantle. Mixing calculations indicate that about 15 to 20 wt% of lower crustal contamination plus variable upper crustal contamination is required to explain the variations of Sr-Nd isotopes in the Shitoukengde intrusion. Significant crustal contamination is also supported by the mineralization at Shitoukengde having high (187Os/188Os)i (0.24 to 4.51) and γOs(t) values (0.24 to 2534) that are comparable to or higher than those of the important Ni-Cu deposits worldwide. Current results provide evidence that assimilation of crustal sulfur at deep crust and siliceous material with variable crustal contamination during magma ascent and emplacement played critical roles in the attainment of sulfide saturation in the parental magma and the formation of the Shitoukengde deposit.