A calcium precipitating and denitrifying bacterium H12 was used to investigate the F removal performance and mechanism. The results showed that the strain H12 reduced 85.24% (0.036 mg·L·h) of F, 62.43% (0.94 mg·L·h) of Ca, and approximately 100% of NO over 120 h in continuous determination experiments. The response surface methodology analysis demonstrated that the maximum removal efficiency of F was 88.98% (0.062 mg·L·h) within 72 h under the following conditions: the initial Ca concentration of 250.00 mg·L, pH of 7.50, and the initial CHNaO·6HO concentration of 800.00 mg·L. The scanning electron microscopy images, the X-ray photoelectron spectroscopy, and X-ray diffraction results suggested the following removal mechanism of F: (1) the bacteria, as the nucleation site, were encapsulated by bioprecipitation to form biological crystal seeds; (2) Biological crystal seeds adsorbed F to form Ca(PO)F and CaF; (3) Under the induction of bacteria, calcium, fluoride and phosphate coprecipitated to form Ca(PO)F and CaF. In addition, the gas chromatography data indicated that F had little or no effect on the gas composition during denitrification, and the fluorescence spectroscopy analysis also proved that the extracellular polymeric substance (protein) is the site of bioprecipitation nucleation.