The Miaoshan is a Cu polymetallic deposit that was newly discovered from Yangchun Basin of western Guangdong Province. The ore bodies occur in Devonian terrigenous clastic rocks and argillaceous carbonate rocks in stratoid and lenticular forms. By using LA-ICP-MS new technology of situ microanalysis, the authors investigated the trace elements characteristics of pyrite and sphalerite. It shows that the trace elements of pyrite is characterized by rich Se, Te, As, while poor Ni. Its Co/Ni and S/Se ratios indicate that the pyrite is closely related to magmatic hydrothermal type deposit. The sphalerite formed on medium-high temperature condition characterized by rich Mn, In, Se, while poor Ga, Ge and Tl etc. The whole trace elements compositional features of sphalerite is the same as that of some typical foreign skarn deposits (e.g. Baita Bihor, Majdanpek, Ocna de Fier and Valea Seaca). Partial trace elements ratios (such as Zn/Cd, Ga/In etc.) and related diagrams (such as Ge-In, Ge-Se etc.) of the sphalerite indicate that the genesis of Miaoshan Cu polymetallic deposit is agreement with skarn-type deposits. S isotopic results show that δ34S value of the ores is more concentrated (-0.4‰ ~ +2‰), with an average at 0.69‰, showing tower-shaped distribution effect, which reflects that the characteristics ore-forming materials originated from magmatic origin. Base on field geological features, coupled with the data of sulfide in situ microanalysis and S isotope, we suggest that the Miaoshan Cu polymetallic deposit belongs to skarn deposits.