Niobium, Zr, REE, and Y are widely enriched in the Upper Permian coal-bearing strata in southwestern China and are regarded as a substantial resource. To better understand the occurrence modes and enrichment mechanisms of these rare metals, comprehensive heavy-mineral separation, Micro-Raman spectroscopy, EPMA, and LA-ICP-MS analyses of primary and secondary metal minerals were conducted in the polymetallic beds in western Guizhou. In addition, the XRD, XRF, and ICP-MS analyses of bulk rocks were carried out. Our results suggest that Nb is primarily hosted in secondary TiO₂ polymorphs which converted from primary Nb-rich rutile, and occurs as minor ilmenorutile and columbite-(Fe). The Zr is sequestered in both detrital zircon and secondary microcrystalline zircon. REE and Y (REY) are mainly incorporated into secondary florencite-(Ce), rhabdophane-(Ce), churchite-(Y), and zircon, also partially adsorbed by clay minerals. The assemblage of detrital zircon, Nb-rich rutile, and discrete Nb minerals reveals that rare metals are preconcentrated during the waning-stage Emeishan alkaline magmatisms. Complex zonings in rutile crystals may result from the diffusion of Nb⁵⁺ and Fe²⁺, and these grains are further overprinted by magmatic-hydrothermal and enveloped by ilmenorutile and columbite-(Fe). Furthermore, magmatic rutile is commonly converted into anatase, brookite, and leucoxene under supergene conditions, and then persisted as stable phases. Authigenic REY-rich (Al)-phosphates and zircon are sourced from the leaching, even decomposition of primary REY-phosphates and zircons. Their colloidal aggregates are precipitated from the acidic and oxidizing low-temperature fluids, which are superposed onto clay matrix. The mineralogical and geochemical features suggest that the polymetallic beds are enriched by both alkaline magmatic-hydrothermal processes in source rocks and supergene fluid alterations in sediments. This study gives new insights into the enrichment processes and conditions, and further extraction of critical metals in the coeval coal-bearing strata in southwestern China.