Kaolinite is often a cause of deformation in soft-rock tunnel engineering, leading to safety problems. The mechanism of the deformation is closely related to the interaction between kaolinite and water molecules. Because kaolinite has multiple defects, the effects of Mg, Ca, and Fe(II) doping on the atomic structure of the kaolinite (001) surface, and the subsequent adsorption and penetration of H2O into the interlayer, were studied systematically using density-functional theory. The results showed that for the Mg-, Ca-, and Fe(II)-doped kaolinites (001), the surface relaxation around the doping layer changed from contraction to expansion, due to the redistribution of electrons. The adsorption energies of the H2O monomer on Mg-, Ca-, and Fe(II)-doped kaolinites (001) were less than on undoped kaolinite (001). The results further revealed that the H2O molecule can also adsorb on the hollow site on the second-layer O surface of the Mg-, Ca-, and Fe(II)-doped kaolinites (001). For the undoped kaolinite, however, the H2O molecule adsorbs on the surface only. The energetic barriers for penetration of H2O from the adsorption site on the surface to the adsorption site on the O surface of Mg-, Ca-, and Fe(II)-doped kaolinites were also calculated: 1.18 eV, 1.07 eV, and 1.41 eV, respectively. The results imply that the influences of Mg, Ca, and Fe(II) doping on kaolinite allow the adsorbed water molecules to penetrate from the on-surface adsorption site to the O-surface site.