The Paleozoic iron oxide copper–gold (IOCG) deposits in Xinjiang correspond to magmatic arc formations (Andean type) within the Central Asian Orogenic Belt (CAOB). These deposits include the Heijianshan, Duotoushan, Shuanglong, and Shaquanzi deposits in the Aqishan-Yamansu belt of Eastern Tianshan, which formed during the inversion of a continental arc-related basin (ca. 310–300 Ma). In contrast, the Laoshankou and Qiaoxiahala deposits along the northern margin of Eastern Junggar formed in an island arc setting (380–370 Ma). Detailed paragenetic studies of these deposits reveal a wide variety of alteration and mineralization patterns, including distinct but typical styles of magnetite and copper–gold mineralization. Fluid inclusion data and isotope tracing of ore-forming fluids indicate the involvement of magmatic-hydrothermal fluids is responsible for the early magnetite mineralization. However, for the late copper–gold mineralization, the deposits formed during the basin inversion have a significant involvement of non-magmatic fluids compared to those of island arc-related deposits. These non-magmatic fluids include basinal brines or residual seawater that reacted with andesitic host rocks. Comparing the IOCG-related magmatic rocks, the regional Bailingshan intrusive complex in the Eastern Tianshan formed during the basin inversion is from more reduced and water-poor parental magma compared to arc magma in the Eastern Junggar. However, the tectonic setting (basin inversion) facilitated the migration and involvement of external fluids, including sulfur, in the mineralization process, potentially compensating for the deficiencies of the magma to generate late economic copper–gold mineralization.