Precious metals can be mobilized during supergene processes, which are important for the formation of high-grade or high-purity ores. The world-class Linglong gold deposit has high-grade ores that have undergone supergene processes in the near-surface zone. Under which conditions the supergene modification occurred and how Au and Ag behaved during the supergene processes have been poorly studied in this deposit. Here, we performed scanning electron microscope (SEM) and laser ablation–inductively coupled plasma–mass spectrometry (LA–ICP–MS) analyses on samples from the supergene enrichment zone of the Linglong gold deposit. The results show that secondary minerals were formed sequentially from magnetite-goethite-limonite to marcasite-acanthite, and finally to siderite after the primary minerals of pyrite-pyrrhotite-chalcopyrite. These mineral assemblages and variations indicate that the supergene modification by groundwater occurred under oxidative and weakly acidic conditions in the near-surface zone and evolved to reductive and near neutral conditions in the supergene enrichment zone. The newly formed marcasite has much higher Au (0.003–23.5 ppm, mean of 1.33 ppm) and Ag (81.7–6021 ppm, mean of 1111 ppm) concentrations than those of the primary pyrite (Au of 0.004–0.029 ppm and Ag of 0.22–4.14 ppm), which together with the formation of independent Ag–S mineral (acanthite), indicates that Au and Ag were significantly mobilized and fractionated during the supergene processes. These processes improved the Au and Ag grades in the supergene enrichment zone and thus facilitate their extraction.