The Tuolugou sedimentary-exhalative (SEDEX) Co-Au deposit is located in the eastern Kunlun metallogenic belt of the northern Qinghai-Tibet Plateau in China. Pyrite is the prevalent Co-hosting sulfide mineral that occurs in the Tuolugou deposit. In this study, we investigated mineral characteristics of Co-bearing pyrite and effect of Co on crystal structure of the pyrite to obtain a better understanding of Co mineralization. Three pyrite generations were identified, including Co-barren pyrite (Py-1, formed during the early mineralization stage I, with Co content of 1-3844 ppm), Co-rich pyrite (Py-2, formed during the sedimentary-exhalative stage II, Co content 15–36522 ppm), and Co-rich pyrite (Py-3, formed during metamorphic stage III, with Co contents of 448–10505 ppm in Py-3A, and 1371–14904 ppm in Py-3B). As Co enters the pyrite structure, it is discovered that the octahedrons in pyrite is twisted and tilted, the lattice parameters (a0) rise, and the sulfur atom positions alter. The Co-rich Py-2 shows a similar REE and trace element distribution as those in quartz albitite, which indicates that Co mineralization is related to SEDEX genesis. Subsequent metamorphism resulted in additional Co enrichment. This detailed study of Co-bearing pyrite provides insights on the details of isomorphism Co in pyrite similar to the situation of this deposit as medium–low Co grade.