Fluoride pollution and water scarcity are urgent issues. Reducing fluoride concentration in water is crucial. Kaolinite has been used to study adsorption and fluoride removal in water and to characterize material properties. The experimental results showed that the adsorption capacity of kaolinite decreased with increasing pH. The highest adsorption of fluoride occurred at pH 2, with a capacity of 11.1 mg/g. The fluoride removal efficiency remained high after four regeneration cycles. The fitting results with the Freundlich isotherm model and the external diffusion model showed that the non-homogeneous adsorption of kaolinite fit the adsorption behavior better. Finally, the adsorption mechanism was analyzed by FT-IR and XPS. The binding energies of various adsorption sites and the chemical adsorption properties of atomic states were discussed in relation to DFT calculations. The results showed that Al and H sites were the main binding sites, and the bonding stability for different forms of fluoride varies, with the size of Al–F (−7.498 eV) > H–F (−6.04 eV) > H–HF (−3.439 eV) > Al–HF (−3.283 eV). Furthermore, the density of states and Mulliken charge distribution revealed that the 2p orbital of F was found to be active in the adsorption process and was the main orbital for charge transfer.