Hydroxyapatite (HAP) is one of the fluoride adsorbents to remove fluoride in water, but F- is hard to enter the lattice of HAP caused by spatial confinement and competitive adsorption, which leads to low defluoridation efficiency. In this study, Ca-deficient regulation method was used to create ion channels during HAP synthesis to overcome the inhibition caused by spatial confinement effect, which increased the defluoridation capacity by 50 % from 1.56 to 2.34 mg/g (Initial F- concentration: 5 mg/L). The effects of dosage, pH, initial F- concentration and co-existing ions on defluoridation process were evaluated and the dosage of 1.4 g/L under neutral condition was the economic condition. The adsorption performance followed the Pseudo-second-order kinetic model and Freundlich isotherm model, which was a spontaneous and endothermic process. The results of molecular mechanics and density functional theory (DFT) calculations showed ion channels near the F- adsorption sites on HAP surface were generated due to the calcium deficiency, which effectively promoted F- into the lattice. The defects also changed the adsorption energy and sites of HF and F-, which reduced the competitive adsorption. In addition, the catalytic decomposition of HF molecules occurred on the surface of HAP was discovered for the first time.