The occurrence of the polymetallic Nb layer in the upper Permian Xuanwei Formation in southwest China has been documented extensively. The origin of Nb, as well as other metals like Zr and rare earth elements (REEs), has received much research attention; however, the source of these elements remains enigmatic. In recent studies, an uncommon Nb-rich titanite (CaTiSiO₅) has been discovered in the Emeishan basalts beneath the Xuanwei Formation in the eastern Yunnan–western Guizhou region. However, its origins and genetic relationship to the polymetallic Nb layer remain unclear. In this study, we used in situ microanalytical and UPb dating techniques to investigate the titanite in these Emeishan basalts. Our objectives were to determine the origins of the titanite and its relationship to the polymetallic Nb layer in the lowermost Xuanwei Formation. The basalts consist of approximately 70%–90% phenocrysts and 10%–30% matrix. The phenocrysts are mainly coarse-grained (>30 μm) plagioclase, clinopyroxene, and Fe-Ti oxides (ilmenite and magnetite), whereas the matrix comprises mainly fine-grained (<30 μm) titanite and glass. The titanite is hypautomorphic or xenomorphic and occurs as small, disseminated grains within the matrix. The titanite U-Pb dating of basalt sample reveals a Tera–Wasserburg lower intercept age of ca. 259.6 ± 4.3 Ma, which corresponds to the age of the eruption timing of Emeishan large igneous province (ELIP; 260.9–257.4 Ma). This implies that the formation of titanite within the matrix can be attributed to rapid cooling of residual melt subsequent to fractional crystallization of a substantial quantity of phenocrysts. The LA-ICP-MS analysis reveals that the trace element composition of titanites in the Emeishan basalts exhibits similarities to weathering-type titanite, as evidenced by elevated La_N/Yb_N ratios and low concentrations of Y, ΣREE, Th, and U, as well as reduced Lu/Hf and Th/U ratios. Thus we propose that these titanites crystallised during the late-stage magmatic evolution, resulting from magmatic fractional crystallization and subsequent weathering alteration. The materials required for titanite crystallization in the basalt matrix primarily sourced from the residual melt, while weathering dissolution of plagioclase and clinopyroxene in the phenocrysts may have provided additional Ca and Eu for titanite formation. As weathering progressed, the Nb-rich titanite underwent a transformation into Nb-rich anatase and gradually became enriched in the regolith. This material was subsequently transported to nearby basins and deposited in terrestrial environments, resulting in formation of the polymetallic Nb layer in the lowermost Xuanwei Formation. Our findings provide insights into the origins and evolution of titanite in the Emeishan basalts, as well as formation of the polymetallic Nb layer in the lowermost Xuanwei Formation in the eastern Yunnan–western Guizhou region, southwest China.