In the present study, a simple method of regenerating microstructure of human tooth under near-physiological conditions (pH 7.0, 37 °C, 1 atm) was developed. Commercial gelatin was used as matrix materials in this method, which nucleated the formation of fluorapatite (FA) nanocrystals and regulated the growth of nanocrystals. As a result, the resulting thin FA coatings had been prepared on human tooth slices and sintered hydroxyapatite disks, which were in tight contact with the substrates. Besides, the morphologies of FA nanocrystals changed from acicular to hexagonal with the exchange cycle of gel increased. Electron dispersive spectrometer analysis indicated that some sodium and carbonate ions were incorporated into the FA crystal lattices and the calcium to phosphorus ratio was approximate 1.58. The mechanical properties of the resulting FA coating were investigated through nanoindentation system, which showed the similar hardness with dentin. In conclusion, this method demonstrated a potential application to repair tooth damage in dental clinics.