Clay minerals are generally used as pivotal indicators to reveal diagenetic parameters such as temperature and pH in hydrothermal ore-forming systems. Within the Late Permian Nb-Zr-REY-Ga-mineralized horizons in eastern Yunnan, the elevated enrichment of critical metals has been considered to be closely associated with abundant clay minerals. In this paper, the identification, abundance, morphology, modes of occurrence, and chemical compositions of two phyllosilicate minerals, namely chamosite (chlorite group) and berthierine (serpentine-kaolinite group) were analyzed by XRD (X-ray diffraction) and SEM-EDS (scanning electron microscopy equipped with an energy dispersive X-ray spectrometer). The results show that chamosite mainly occurs as massive and book-like aggregates, while berthierine occurs in various forms, including coarse granular, spherulitic, sheaf-like, sharp-angular, and vermicular aggregates. The modes of occurrence and scatter plots of Mg/(Mg + Fe) vs. Al/(Al + Fe + Mg) of chamosite indicate a Fe-Mg-rich siliceous hydrothermal origin. In the Al/Si-Mg/Fe diagram, analysis points for berthierine are distributed in the partially overlapping fields of hydrothermal ore, laterite/bauxite, and marine, indicating that the formation of berthierine was influenced by various geological factors. Based upon its chemistry and modes of occurrence, berthierine mainly originated by direct precipitation from Fe-Mg-rich siliceous hydrothermal fluids, but in some cases, it was derived from the replacement of precursor minerals and the in-situ alteration of volcanic fragments. A scenario of the transformation mechanism of clay minerals in the Nb-Zr-REY-Ga-rich horizons is proposed. Airborne volcanic glasses and primary minerals were initial altered in-situ into vermicular kaolinite and angular berthierine in the early diagenetic stage. Subsequently, some vermicular kaolinite and the oolitic berthierine crystallized from solutions underwent gradual illitization, and some pre-existing minerals (e.g., albite, kaolinite, and illite) were altered into berthierine, while a proportion of chamosite transformed from berthierine through an interstratified berthierine/chamosite (B/C) in the middle to late diagenetic stages. Throughout all stages of diagenesis, the chamosite, berthierine, and their intermediate phases precipitated directly from Fe-Mg-rich siliceous hydrothermal fluids. Moreover, the diagenetic temperature revealed by chamosite is from ∼200 to ∼302℃, indicating that the Nb-Zr-REY-Ga mineralization and chamosite formation occurred under low-temperature thermal alteration conditions.