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The distortion process of kaolinite annealed from 25 °C to 550 °C for different holding times can be characterized using a thermogravimetric/differential scanning calorimeter (TG/DSC) for thermal analysis, X-ray diffraction (XRD) for establishing the crystal structure, the Fourier transform infrared spectrum (FTIR) for identifying the functional groups, and a scanning electron microscope (SEM) for establishing the microstructure. Dehydroxylation is the main reaction during annealing from 25 °C to 550 °C and leads to kaolinite crystal distortion. A stable crystal structure during distortion was obtained by optimizing the bulk phase with quantum chemistry. Then, the crystal structure was studied by using ab initio multiple scattering calculations for X-ray absorption of the fine structure (XAFS). The results of X-ray absorption near the edge structures (XANES) determined that peak shifts and intensity phases slightly increased. The crystal structure distortion of kaolinite during annealing can be explained by the experimental and simulation results. This work provides theoretical support for identifying kaolinite with different degrees of distortion and has the potential for further developments in coal gangue separation.