[Display omitted] • Mineral composition of bauxite is affected by karstic topography. • Bauxite formation conditions range from oxidation to reduction. • Minerals deposited under different conditions are rich in microorganisms. • Microorganisms may promote the deposition of diaspore and boehmite. The metallogenic process of karstic bauxite in Central Yunnan Basin (CYB) remain obscure. Mineralogical, geochemical, and isotopic analyses of two profiles (profile A and B) in the Yuxi karstic bauxite deposit within CYB were conducted to explore the formation environment and metallogenic process of Early Permian bauxite. Profile A in the karstic uplifted area comprises clayey bauxite, claystone, and oolitic bauxite from the bottom to the top, while profile B in the karstic depression area contains oolitic bauxite, claystone, oolitic bauxite, and claystone. The oolitic bauxite mainly contains diaspore and chamosite, and a small amount of kaolinite and anatase, while the clayey bauxite primarily includes boehmite and kaolinite, and a small amount of goethite and anatase. The claystone is dominated by kaolinite and illite. The δ15N value of the oolitic bauxite in the top of profile B is close to zero (−0.8 ‰), indicating a reducing deposition environment. The δ13C org value of profile A is negatively shifted between clayey bauxite and oolitic bauxite, while that of profile B is not significantly changed between the lower oolitic bauxite and the upper oolitic bauxite. This indicates that REDOX changes in the formation of clayey bauxite and oolitic bauxite in profile A are obvious, while REDOX changes in profile B are not evident. Mineral assemblages and isotopic results suggest that the mineralization conditions of profile A experienced a transition from oxidizing and weakly alkaline to reducing and alkaline, while the mineralization conditions of profile B were always reducing and alkaline. The presence of large-scale microorganisms, negative δ34S values (−42.2 to −10.1 ‰), and framboidal and cuboidal goethite provide evidence for microbial involvement in the entire mineralization process. The above results confirm two metallogenetic events of Yuxi karstic bauxite deposit. In the early metallogenetic event, the water table was low and most of the karstic terrains were exposed except some karstic depressions. Abundant boehmite and kaolinite thus formed in the karstic uplifted areas forming the clayey bauxite, and diaspore and chamosite in the karstic depressions forming the oolitic bauxite. In the late metallogenetic event, with the rise of water table, all karstic terrains were submerged, and large-scale diaspore and chamosite were widely deposited, thus forming oolitic bauxite.