The microstructure characterizations of pyrophyllite were investigated by using field emission scanning electron microscopy (FE-SEM), high-resolution transmission electron microscopy (HRTEM) coupled with selected area electron diffraction (SAED), X-ray diffraction (XRD) and X-ray Fluorescence (XRF). The results are obtained: 1) major constituents of natural mineral from Qingtian pyrophyllite deposit are pyrophyllite and quartz, and the 2M-pyrophylite is corroborated well; 2) a complex laminal structure of the micro-crystal of pyrophyllite is found, and the thickness of flake microstructure is (8±2) nm; and 3) high energy electron beam irradiation induces morphology of clay mineral particles and lattice structure change, and it results in lattice dilatation and transformation from crystalline to amorphous finally.