The Yundukala deposit is a newly discovered Au–Cu–Co deposit located in the northern margin of Junggar in the Central Asian Orogenic Belt. The Au–Cu–Co mineralization is associated with the contact zone between a dioritic intrusion and basalt. The formation of the vein mineralization can be divided into three mineralization stages: chlorite + pyrite, quartz + polymetallic sulfide, and quartz + calcite. Ore microscopy and in-situ laser ablation inductively coupled plasma mass spectrometry were used to investigate textural and compositional relationship between pyrite, chalcopyrite, arsenopyrite, and cobaltite. The gold in the deposit is present in two main mineralogical forms: native gold (micron inclusions of the gold) and invisible gold (solid solution of gold). Cobalt in the vein mineralization is primarily associated with cobaltite, whereas pyrite, chalcopyrite, arsenopyrite, and pyrrhotite contain small amounts of cobalt. There is a positive correlation between As and Au in Py-Ⅱ (R2Au-As = 0.9211; R2Au-As = 0.4306) and cobaltite and a positive correlation between Co and Au in cobaltite (R2Au-Co = 0.8168). This relationship supports a model in which arsenic plays a role in the occurrence of gold. The correlation of trace elements in minerals and the formation sequence and interpenetration relationship between minerals indicate the progressive geochemical evolution of a single ore-forming fluid arising from a single vein mineralizing event. Hydrothermal processes led to alteration of the surrounding rocks while simultaneously extracting Au, Cu, and Co, forming ore-forming fluids. As physical conditions changed, minerals began to precipitate, ultimately resulting in the formation of ore deposits during the Carboniferous period (354–353 Ma).