Based on comprehensive petrological, geochronological, and geochemical studies, this study analyzed the relationships between the Beiya gold-polymetallic skarn deposit and quartz syenite porphyries, and discussed the source(s) and evolution of magmas. Our results suggest that syenite porphyries (i.e. the Wandongshan, the Dashadi, and the Hongnitang porphyries), which formed between the Eocene and the early Oligocene epochs, are the sources for the gold-polymetallic ores at the Beiya deposit. Carbonate rocks (T2b) of the Triassic Beiya Formation in the ore district provide favorable host space for deposit formation. Fold and fault structures collectively play an important role in ore formation. The contact zone between the porphyries and carbonates, the structurally fractured zone of carbonate and clastic rocks, and the zone with well-developed fractures are the ideal locations for ore bodies. Four types of mineralization have been recognized: 1) porphyry-style stockwork gold–iron (copper) ore, 2) skarn-style gold-iron (copper and lead) ore in the near contact zone, 3) strata-bound, lense-type lead–silver–gold ore in the outer contact zone, and 4) distal vein-type gold–lead–silver ore. Supergene processes led to the formation of oxide ore, such as the weathered and accumulated gold–iron ore, the strata-bound fracture oxide ore, and the structure-controlled vein-type ore. Most of these ore deposits are distributed along the axis of the depressed basin, with the hypogene ore controlling the shape and characteristics of the oxide ore. This study provides critical geology understanding for mineral prospecting scenarios.