We investigated the causes of distortions and the influence of hydrogen bonding on these distortions in kaolinite. We used CLAYFF supplemented with fluorine potential parameters for the energy minimization modeling of different molar fractions of fluorine substitution for interlayer hydroxyls. Results show that the reasons for tetrahedral basal oxygen corrugation are Al—O (connected oxygen) bond stretching because of the misfit between tetrahedral and octahedral sheets and the requirement of the tetrahedron to maintain its shape. The reason for tetrahedral rotation is similar to Newnham's explanation. The counter-rotation of the upper and lower triads in the octahedron results from: (1) the misfit between tetrahedral and octahedral sheets, specifically the increase in the O—Al—O angle (θ1) and the Al—O—Al angle (θ2) between connected oxygens/inner hydroxyl oxygens and Al, the O—Al—O angle (θ4) and the Al—O—Al angle (θ5) between the interlayer hydroxyl oxygens and Al, and a decrease in the octahedral co-edge O—Al—Oangle(θ3); (2) the decrease in θ1, θ2 and the increase in θ3 because of the repulsion between Al and Si; (3) restructuring caused by the bond angles in (1) and (2); (4) the special network structure of kaolinite. In addition, the shortening of the octahedral O-O co-edge and the approach of Al to the interlayer hydroxyl oxygen also result from effects (1)-(4). Octahedral flattening results from an increase in θ1, θ2, θ4 and θ5 and from a decrease in θ3. The interlayer hydrogen bonds inhibit tetrahedral basal oxygen corrugation, octahedral flattening and the counter-rotation of the upper and lower triads in the octahedron, but it has an opposite role during tetrahedral rotation. Furthermore, when the fluorine content is low (xF=0-0.7), an increase in the interlayer distance is not obvious with an increase in fluorine content and this confirms that ammoniumfluoride may not be necessarily involved in the hydration of kaolinite.