Niobium in kaolin clay from the Late Permian sequences was reported in the range of several hundreds of micrograms per gram and was considered as a potential resource for its high concentrations and large areal distribution. Ti-bearing minerals associated with kaolin clay were identified as the main host phase for niobium in some case studies. However, the correlation between the concentration of niobium and titanium is poor, and the types of Ti-bearing minerals and modes of occurrence of niobium are not clear. Typical kaolin clay samples from the Late Permian sequences from southwest China were characterized, and the final products derived from kaolin clay sample were investigated using XRF, ICP-MS, XRD, SEM, and TEM (EDS). The results reveal that there were three types of TiO2 mineral phases in the clay samples: (a) massive TiO2 minerals and (b) aggregates of nano TiO2 minerals did not contain niobium while (c) granular TiO2 minerals were the source of niobium from the EDS analysis. The granular TiO2 minerals included anatase and rutile, both of which were the sources of niobium in kaolin clay in the current study. The findings are of great theoretical implication for source and origin study of Ti-bearing minerals and guidance for separation and recovery of niobium from kaolin clay.