The Lindai bauxite deposit with typical sequence of carbonaceous shale- bauxite- iron rock occurs in the Jiujialu Formation of the Lower Carboniferous. With the roof and floor of bauxite as the main research objective, this study investigated top carbonaceous shale, bottom purple mudstone and karst feature using geochemistry methods and paleontological identification, as well as field survey. The results show that the top carbonaceous shale contains abundant pyrite and plant fossils, and minor animal fossils. The plant fossils are mainly archaeocalamites scrobiculatus and sublepidodendron, the assemblage of which suggests that the bauxite deposit likely formed in the Early Carboniferous. Brachiopods and gastropods fossils discovered in dolomite interlayer indicate that the carbonaceous shale formed in a coastal environment. This also suggests that the Lindai bauxite deposit deposited in offshore lake environment. The study performed an immersion test on samples from pyrite carbonaceous shale in distilled water. The results show that the immersion liquid presents strong acidity with pH values of 1.5~2. According to overlaying relationship of strata (the top carbonaceous shale and bauxite) in Lindai, Maochang and Xiaoshaba mines, this study found that the overlying carbonaceous shale after the formation of bauxite removed Si and Fe out of underlying bauxite layers under the leaching effect of meteoric water, thus improving the grade of bauxite ore deposits. Discovery of strong weathering sandy dolomite, dissolution cracks, calcium junction and lacustrine sediments suggests that the purple red mudstone within Cambrain dolomitic rock was likely the source rock for bauxite mineralization and has some significance for exploration.