The Huangshannan Ni–Cu (–PGE) sulfide deposit, a new discovery from geological prospecting in Eastern Tianshan, is in a belt of magmatic Ni–Cu (–PGE) sulfide deposits along the southern margin of the Central Asian Orogenic Belt. The host intrusion of the Huangshannan deposit is composed of a layered ultramafic sequence and a massive gabbro–diorite unit. The major sulfide orebodies occur mainly within websterite and lherzolite in the layered ultramafic sequence. In-situ zircon U–Pb dating analyses yielded a crystallization age of 282.5±1.4Ma, similar to the ages of the Permian Tarim mantle plume. Samples from the Huangshannan intrusion are characterized by nearly flat rare earth elements patterns, negative Zr, Ti and Nb anomalies, arc-like Th/Yb and Nb/Yb ratios, and significantly lower rare earth element and immobile trace element contents than the Tarim basalts. These characteristics suggest that the Huangshannan intrusion was not generated from the Tarim mantle plume. The primary magma for the Huangshannan intrusion and its associated sulfide mineralization were formed from different pulses of picritic magma with different degrees of crustal contamination. The first pulse underwent an initial removal of 0.016% sulfide in the deep magma chamber. The evolved magma reached sulfide saturation again in the shallow magma chamber and formed sulfide ores in lherzolite. The second pulse of magma reached a level of 0.022% sulfide segregation at staging chamber before ascending up to the shallow magma chamber. In the shallow conduit system, this sulfide-unsaturated magma mixed with the first pulse of magma and with contamination from the country rocks, leading to the formation of sulfide ores in websterite. The third magma pulse from the deep chamber formed the unmineralized massive gabbro–diorite unit of the Huangshannan intrusion.