Skarn Au deposits are particularly developed along Middle and Lower Yangtze River region, eastern China, but gold behavior and genesis of the skarn Au deposits remain unclear. Whole-rock geochemical, sulfur isotopic and in-situ mineralogical data from the mineralized alteration stages of Chaoshan skarn Au deposit in Tongling region are systemically investigated to reveal Au distribution and precipitation, and useful information for ore-forming process. The altered rocks and ores in the Chaoshan deposit have total REE contents of 7.81–226 ppm and show LREE enrichment patterns with weak negative to positive Eu (δEu = 0.71–2.24) anomalies. Electron probe microanalysis results indicate that garnet and pyroxene of the Chaoshan deposit are grossular-andradite and diopside-hedenbergite series, respectively. In situ elemental compositions of the euhedral pyrite analyzed show that invisible Au is mainly of lattice-bound Au+ in As-bearing pyrite. The studied pyrite samples also have high Co/Ni (mainly >1) and Se/Tl (>10) ratios, highly variable Pb and As contents, low Se content (<5.00 ppm), low Tl/Pb and Sb/Pb ratios, and relatively consistent sulfur isotopic compositions (5.0–8.3 ‰). The distinctly geochemical characteristics indicate that the Chaoshan skarn Au mineralization was likely derived from a magmatic-hydrothermal system. A comprehensive discriminant analysis shows that the Au precipitation and enrichment of the Chaoshan deposit are a result of boiling-induced trace element fractionation resulted from fluid boiling during the skarn formation process.