The Lalingzaohuo cobalt-bearing Cu polymetallic skarn deposit, located in the central part of the East Kunlun Orogenic Belt, is mainly hosted in the Paleoproterozoic Jinshuikou Group. The occurrence and genesis of cobalt at Lalingzaohuo were investigated by field geology, mineralogy, geochronology, and electron probe microanalyses (EPMA), that these data provide some insights into the ore-forming process and also show the key characteristics of a cobalt-bearing skarn. Garnet U-Pb dating yielded a lower intercept 206Pb/238U date of 207.5 ± 4.9 Ma, younger than spatially related quartz diorite (SHRIMP zircon U–Pb dating, 246.8 ± 1.7 Ma), which suggested that the Lalingzaohuo was formed during the Late Triassic. Photomicrographs and EPMA data confirm that Co mineralization is associated with metal sulfides, which develop at the sulfide stage. Cobalt occurrence in Lalingzaohuo is restricted to Co mineral (cobaltite) and other metal sulfides (pyrite, pyrrhotite, chalcopyrite, and sphalerite) where isomorphic substitution occurred. Cobaltite is mainly distributed at the periphery of the skarn alteration zone with more pyroxene. The isomorphic substitution content of Co in pyrite (2.43–3.05 wt%), pyrrhotite (1.87–2.47 wt%), chalcopyrite (0.63–1.38 wt%), and sphalerite (0.73–0.90 wt%) is high. The negative correlation between Co + Ni (wt.%) and Fe (wt.%) suggests that Co + Ni replaces Fe in pyrite and pyrrhotite. The weak correlation between Co (wt.%) and Cu or Fe (wt.%) indicates that only part of the isomorphic Co in chalcopyrite is carried out by substituting Fe and Cu. The high Fe and Co content in sphalerite indicate that Co + Fe replaces Zn by isomorphic substitution. The isomorphic substitution of Co in the Lalingzaohuo deposit is an important potential available resource. Based on the magmatic activity records, the Triassic Lalingzaohuo deposit was formed under an extensional environment, which is related to the subduction of the branch of the Paleo-Tethyan Ocean. This study together with the regional developed cobalt-bearing skarn deposits indicates that the East Kunlun Orogenic Belt is an important cobalt-bearing skarn mineralization potential region.