In this paper, 28 bedded chert samples (3 samples from the Maokou Formation of the Middle Permian and 25 samples from the Heshan Formation of the Upper Permian) were analyzed for major and rare earth elements. The authors considered that bedded cherts from the Heshan Formation in the Penglaitan section deposited in marginal sea basin environment influenced by terrigenous materials and silica of them derived from siliceous organism as biogenic origin, whereas, those from the Maokou Formation deposited in marginal sea basin environment without influence of terrigenous materials and silica of them primarily derived from hydrothermal fluid as hydrothermal origin. Comparing sedimentary background of bedded cherts in the Penglaitan section with those as hydrothermal origin in the Tieqiao section, this study showed that Laibin area developed a marginal sea basin environment rich in silica during the Middle-Late Permian and discrepancy in influence of terrigenous materials controlled the different origin of bedded cherts in Laibin area.