A large amount of bedded chert widely deposited during the Ordovician and Silurian transition in South China. In this study, analyses of the petrographic characteristics, the major elements and rare earth elements (REEs), were conducted on 31 bedded chert samples obtained from the Wufeng and Longmlaxi Formations at the Qiliao section in the Shizhu area of the Sichuan Basin to determine the sedimentary environment and the origin of the bedded chert during the Ordovician and Silurian transition. The following conclusions were obtained: (i) the bedded chert in the Wufeng and Longmaxi Formations at the Qiliao Section originated mainly from terrigenous input and siliceous organisms and was slightly influenced by hydrothermal fluid, (ii) siliceous organisms were a key factor controlling the differences in the SiO2 content of the bedded chert in the Wufeng and Longmaxi Formations at the Qiliao Section, and (iii) the bedded chert in the Wufeng and Longmaxi Formations deposited in a continental margin environment during the Ordovician and Silurian transition.