Western Yunnan is the well-known polymetallic province in China. It is characterized by copper-gold mineralization related to Cenozoic alkali-rich porphyry. This paper analyzes the silicon isotope data obtained from four typical alkali-rich porphyry deposits based on the dynamic fractionation principle of silicon isotope. The study shows that the ore materials should originate mainly from alkali-rich magmas, together with silicon-rich mineralizing fluids. The process of mineralization was completed by auto-metasomatism, i.e. silicon-rich mineralizing fluids (including alkali-rich porphyry and wall-rock strata) replaced and altered the country rocks and contaminated with crustal rocks during the crystallization of alkali-rich magmas. Such a process is essentially the continuance of the metasomatism of mantle fluids in crust's mineralization. This provides important evidence of silicon isotopic geochemistry for better understanding the mineralization of the Cenozoic alkali-rich porphyry polymetallic deposits