The surface properties of kaolinite were determined using density functional theory discrete variational method (DFT-DVM) and Gaussian 03 program. A SiO4 tetrahedral hexagonal ring with two Al octahedra was chosen to model the kaolinite crystal. The total density of states of the kaolinite cluster are located near the Fermi level at both sides of the Fermi level. Both the highest occupied molecular orbit(HOMO) and the lowest unoccupied molecular orbit (LUMO) of kaolinite indicate that kaolinite system can not only readily interact with electron-acceptor species, but also readily interact with electron-donor species on the edge surface and the gibbsite layer surface, and thus, shows amphoteric behavior. Substitution of Al3+ for Si4+ in the tetrahedral site linking the vacant Al3+ octahedra does not increase the surface chemical reactivity of kaolinite, while substitution of Al3+ for Si4+ in the tetrahedral site with the apex O linking Al3+ octahedra increase the surface chemical reactivity of the siloxane surface of kaolinite, especially acting as electron donors.Additionally, substitution of Al3+ for Si4+ in the tetrahedral site results in the re-balance of charges, leading to the increase of negative charge of the coordinated O atoms of the AlO4 tetrahedra, and therefore favoring the formation of ionic bonds between cations and the surface O atoms in the basal plane.