The Huangyangshan super-large graphite deposit is located in the Qitai area of East Junggar in Xinjiang Province, China. This deposit is well known for its distinguishing properties, including the alkaline granite complex that hosts the graphite ore, the dominantly orbicular structure developed in the graphite ore, and the association of graphite with metal sulfides in the orbicular ore. This study aims to determine the genetic relationship between graphite and metal sulfides in order to better understand the graphite mineralization process of the Huangyangshan deposit. The methods applied in the study include X-ray micro-CT scanning and scanning electron microscopy (SEM) analyses of the orbicular graphite ore and in situ inductive laser ablation-coupled plasma mass spectrometry (LA-ICP-MS) trace element analyses of the pyrrhotite and chalcopyrite associated with the graphite. The analytical results show that the graphite ore is composed of crystalline graphite, K-feldspar, albite, quartz, biotite, amphibole, and metal sulfides. The metal sulfides in the orbicular ore include pyrite, pyrrhotite, pentlandite, and chalcopyrite. According to the color, crystalline shape, texture, and occurrence, pyrrhotite can be classified into four types (I, II, III, and IV), and chalcopyrite into two types (I and II), of which types I, II, and III pyrrhotite and type I chalcopyrite have a close genetic relationship with graphite. The granular types (I, II, and III) of pyrrhotite are enriched in Co, Ni, Se, Ge, and Te and are depleted in As, Sb, Ag, and Au; they also have a high value of Co/Ni, indicating that these types of pyrrhotite have a magmatic origin. Low values of Co/Ni suggest that type IV pyrrhotite has a hydrothermal origin. The similar contents of Co and Ni and the values of Co/Ni compared with the chalcopyrite from the magmatic Co–Ni sulfide deposits imply that type I chalcopyrite has a magmatic origin. In summary, the metal sulfides of the Huangyangshan deposit are genetically related to graphite mineralization and formed predominantly by magmatic processes.