The Mangyahedong gold deposit—recently discovered in the Qimantage segment of the East Kunlun orogenic belt—is a high-priority exploration target. Key unknowns include its mineralization age, the sources of sulfur and gold, and the tectonic–magmatic–hydrothermal controls on formation. These gaps have hindered genetic classification and stage-specific research. We addressed them through integrated petrography, TIMA mineral mapping, in situ LA-ICP-MS analysis of pyrite from three mineralization stages, and U-Pb dating of hydrothermal apatite spatially and temporally linked to the main sulfide-precipitation event. The stages are: (I) early sericite–quartz alteration; (II) main ore stage—carbonate–chlorite–sulfide + native gold; and (III) late calcite–pyrite veins. Pyrite zoning shows that early pyrite cores are enriched in As and Au. In contrast, the main-stage pyrite has As-poor cores, with As, Au, and Co progressively enriched toward the rims. This zoning pattern indicates evolving fluid redox conditions and metal complexation during ore deposition. A ²⁰⁷Pb/²⁰⁶Pb age of 406 ± 13 Ma from apatite in gold-bearing quartz–sulfide veins constrains gold deposition to the Late Silurian–Early Devonian transition. Age, texture, and geochemistry collectively support a regional metamorphic–deformational origin, consistent with the orogenic gold model. Isotopic and elemental data point to the Qimantage Group volcanic rocks as the dominant source of ore-forming elements—indicating strong potential for discovery along strike and at depth.