The East Kunlun orogenic belt is one of the most important Co-rich polymetallic metallogenic belts in China. Niukutou, a typical Pb-Zn-(Fe) skarn deposit, is situated within the marble formations of the Ordovician-Silurian Qimantagh Group in this belt. Six distinct stages of mineralization have been identified: (1) prograde skarn stage, (2) hydrous mineral-oxide stage, (3) pyrrhotite stage, (4) chalcopyrite stage, (5) sphalerite-galena stage, and (6) carbonate stage. Co enrichment predominantly manifests at chalcopyrite stage, with two distinct Co minerals identified: glaucodot and cobaltite. Co is also present as isomorphous substitution in sulfides (mostly arsenopyrite) and as inclusions in chalcopyrite. Variations in As and S contents in arsenopyrite suggest a steady decrease in ore-forming fluid temperature from the pyrrhotite stage to sphalerite-galena stage. Variations in the Co, Ni, Se, As, Sb, Cu, Sn, Ag, and Zn contents in pyrite indicate fluctuations in temperature, oxygen fugacity, and fluid composition during ore formation. Sulfur isotope compositions (δ34S) through the pyrrhotite stage to the sphalerite-galena stages show a limited range from +3.4 to +7.0 ‰, suggesting a predominantly magmatic source. Whereas, the δ34S of pyrite and marcasite in carbonate stage exhibit significant variations from −22.5 to +22.7 ‰. We propose that this significant variation may be caused by mixing of sulfur from the surrounding rocks and the large fluctuations in oxygen fugacity due to the influx of meteoric water at the carbonate stage. Overall, Co in Pb-Zn skarn system may occur either as independent minerals or as lattice substitution in sulfides such as arsenopyrite. The deposition of Co-bearing minerals is related to decreases in temperature and fO2 during the chalcopyrite stage.