We analyzed sulfur isotopes, trace elements and chalcophile elements (Se, Te, As, Sb, and Hg) in the native sulfur matrix from the Kueishantao hydrothermal system and conducted a systematic micro-analytical investigation. The sulfur matrix lacked all measured metals (e.g., Fe, Cu) and rare earth elements (REEs) while being significantly enriched in Te, As, Se (750–1500 ppm), Sb (around 100 ppm) and some Hg. The δ34S data (0.2–2.4‰) suggest a magmatic source leached from igneous rocks and a small contribution of seawater sulfates to the sulfur in hydrothermal deposits. Correlations between Te, As, Sb, and S (r2 = 0.30–0.61) indicate that these elements behave coherently in magmatic-hydrothermal processes. The enrichment factors and content ratios of these elements demonstrate their abundance in the sulfur matrix and minor fractionation after being partitioned into the metallic melt and forming a separate vapor phase to transport. Our study focuses on the native sulfur matrix in a shallow-water volcanic hydrothermal system, to which relatively little attention has previously been paid. This will expand our understanding of hydrothermal precipitates. The study of volatile chalcophile elements in the matrix will provide significant information about their sources, distributions and other geochemical behaviors in magmatic-hydrothermal processes and help to understand the Kueishantao hydrothermal circulation better.