The clay mineralogy of pyroclastic Nb(Ta)-Zr(Hf)-REE-Ga mineralization in Late Permian coal-bearing strata from eastern Yunnan Province; southwest China was investigated in this study. Samples from XW and LK drill holes in this area were analyzed using XRD (X-ray diffraction) and SEM (scanning electronic microscope). Results show that clay minerals in the Nb-Zr-REE-Ga mineralized samples are composed of mixed layer illite/smectite (I/S); kaolinite and berthierine. I/S is the major component among the clay assemblages. The source volcanic ashes controlled the modes of occurrence of the clay minerals. Volcanic ash-originated kaolinite and berthierine occur as vermicular and angular particles, respectively. I/S is confined to the matrix and is derived from illitization of smectite which was derived from the original volcanic ashes. Other types of clay minerals including I/S and berthierine precipitated from hydrothermal solutions were found within plant cells; and coexisting with angular berthierine and vermicular kaolinite. Inferred from the fact that most of the I/S is R1 ordered with one case of the R3 I/S; the paleo-diagenetic temperature could be up to 180 °C but mostly 100–160 °C. The micro-crystalline quartz grains (<10 µm) closely associated with I/S were observed under SEM and were most likely the product of desiliconization during illitization of smectite.