Abstract：Chert is widely distributed on the bottom of the Upper Permian Heshan Formation in western Guangxi. The chert layers extend stably on the lateral side, and the bed surfaces are smooth. The authors measured three sections： the north Shanying Village section and the north Xinxu Village section in Taiping Town, Pinguo County, and the Donglan section in Donglan County. In the laboratory the authors conducted the microscopic examination and rare earth element analysis of the chert. The results show that all the chert is rich in organisms such as spongy spicules, foraminifers, and algae, which are well preserved. The low content of rare earth elements is similar to that of sea water, with the slight loss of light rare earth elements and insignificant Ce negative anomaly. According to the characteristics of the rare earth elements and bioassemblages of the chert, the authors hold that the chert on the bottom of Heshan Formation was formed in shallow water and belonged to a relatively closed environment of continental margin; the silicon of the chert occurred in mixed meteoric-marine coastal systems, without the addition of volcanic components and hydrothermal solution. the occurrence of chert indicates that the rapid transgression in late Permian resulted in the increase of the depth of water in western Guangxi, especially along the Xinxu Village section, where the platform was largely submerged, and the water was clean, which was suitable for the breeding of such living things as sponges, foraminiferas, brachiopodas, and gastropods and was hence favorable for the development of chert and limestone.