Permian karstic bauxite and its Quaternary derivative, in western Guangxi, southwestern, South China Block, possess a total tonnage greater than 0.5 billion tons. The primary late Permian karstic bauxite formed in reduced environment in the background of Tethyan accretionary orogenesis. And as one consequence of Cenozoic convergence of the Indian and Eurasia continents, the primary orebody was uplifted, eroded and re-sedimented within Quaternary laterite. The geochemical variation and its controls during the ore transformation from Permian to Quaternary remain poorly understood. Quaternary ore blocks comprise an inner zone of fresh ore, and then it gradually transited through a middle zone to a margin with extensive weathering. One such bauxite block was selected and further subdivided into twenty-three samples for geochemical and mineralogical analysis. The inner and middle zones contain similar mineralogical compositions, dominated by diaspore and amesite, with minor illite, anatase, goethite, pyrite, zircon, and rutile. The margin is composed of diaspore, with small amounts of amesite, boehmite, illite, goethite, anatase, kaolinite, zircon, rutile, and barite. Bauxite in all three zones is composed of mainly Al, Si, Fe, and Ti, and high contents of Zr, Cr, Li, F, S, Zn, V, Sr, Nb, Ba, and REE. Variations in Fe2+ and Fe3+ between the three zones were observed. The elements Si, Al, Fe2+, Mg, Ba, Cr, F, Li, Ni, Zn, and REE decrease from the core of the ore block outwards, corresponding to an increase in S and Fe3+. Depletions in Si, Al, Fe2+, Mg, Ba, and Cr were caused by the dissolution of amesite. Most of the Al and Si in amesite were lost during the weathering, and minor retained to form kaolinite. Depletions in Li, Ni, and Zn resulted from changes in the depositional environment between the late Permian and Quaternary. Dissolution of REE-bearing fluorocarbonates resulted in depletions of REE and F. The enrichment of Fe3+ and S was related to the precipitation of goethite, hematite, and barite in an oxidizing environment, while local enrichment of Ce resulted from the redox change of Ce3+→Ce4+ under the same condition. This shows that the chemical composition of laterite enwrapping the bauxite also took part in Quaternary bauxite transformation. This study shows that the elements migrations during bauxite transformation were influenced by multiple independent factors except for the elemental attributes.