Elevated concentrations of uranium have been found in many bauxite deposits, but the status of uranium in the ores and the mechanisms of enrichment have not been well understood. In this paper, we report a new case of uranium enrichment in a paleo-karstic bauxite deposit at Yunfeng, southwestern China, present electron probe micro-analyzer (EPMA) and Raman spectroscopic evidence for the presence of separate U-minerals, and propose a model in which uranium was enriched through successive processes from chemical weathering through early to burial diagenesis. The Yunfeng bauxite ores, developed in Lower Carboniferous mudrocks overlying Middle to Upper Cambrian carbonate rocks, contain 18.0 to 62.4 ppm (average 35.1 ppm) U, which is much high than the abundances in average crustal rocks (1–3 ppm). Micron-sized uraninite occurs as rims of Ti-oxides, fillings of micro-fractures in kaolinite, and disseminated grains in association with sulfides in the matrix of diaspore and kaolinite. Trace and rare earth elements analysis indicates that the bauxite ores could not be produced by in-situ weathering of the carbonates underlying the orebodies. Instead, the precursor rocks of the bauxite ores are inferred to be black shales originally enriched in uranium that were exposed tens of kilometers away. Detrital grains of the black shales were transported and accumulated in depressions above karstified carbonates in the Yunfeng area, where they were subjected to intense weathering to form bauxite ores. The weathering of the shale clasts liberated much of the uranium due to oxidation of uranium from U4+ to U6+. However, the majority of the U6+ was reduced to U4+ again due to availability of reducing agents such as organic matter and sulfides originally in the shales, forming nanocrystals of UO2+x in close association with Ti-oxides disseminated in Al-hydroxides and clay minerals. These nanocrystals of UO2+x were converted to uraninite during diagenesis, together with the convention of gibbsite and boehmite to diaspore and the formation of anhedral to euhedral pyrite and various Cu-, Pb-, Ni- and Co-rich sulfides. The recognition of uraninite in the bauxite ores is important for uranium exploration and for evaluation of the economic value of uranium as a byproduct of bauxite deposits.