The Kalatongke Cu-Ni sulfide deposit in northern Xinjiang, northwest China, is located on the southern side of the regional Irtysh fault zone, which is the boundary between the early Paleozoic Altai orogenic belt to the north and the late Paleozoic Junggar terrane to the south. In the Kalatongke region there are 11 mafic intrusions which were emplaced in Lower Carboniferous strata. Economic Ni-Cu sulfide ores are found within three of these intrusions, which are well differentiated, and compositionally zoned. Four rock types are recognized which, from top to base of the three mineralized intrusions, include biotite diorite, biotite-hornblende norite, biotite-hornblende-olivine norite, and biotite hornblende-dolerite. The biotite-hornblende olivine norites and biotite-hornblende norites are the most favorable host rocks for Ni-Cu mineralization. The initial (87Sr/86Sr)t (t = 280 Ma) ratios of the intrusions vary from 0.70375 to 0.70504, and εNd(t) from 6.3 to 8.2, implying that the magmas originated from depleted asthenospheric mantle. However, the strong enrichment of lithophile elements such as K, Rb, Th, U, and LREE, the negative Nb and Ta anomalies, and the high δ18O values of whole rocks (5.4–10.6‰) suggest significant crustal contamination. These patterns are present in almost all samples from the intrusions, indicating that the contamination took place before the magma was emplaced at its present level in the crust. Crustal contamination is interpreted to have driven the magma to S-saturation and brought orthopyroxene onto the liquidus. Convection, or perhaps flow differentiation of the crystal-bearing magma during ascent, caused the dense sulfide melt with entrained olivine and orthopyroxene crystals to become concentrated in the center of the intrusions, whereas the fractionated magmas formed other, less mafic intrusions, which intrude the nearby strata.