The present invention belongs to the technical field of nano-materials, and particularly relates to a preparation method and application of a hydrophilic rare earth nano-material, and the method is as follows: a rare earth nitrate and chloride as rare earth sources, sodium fluoride and ammonia fluoride as fluoride sources, sodium chloride and sodium nitrate as sodium sources, ethylene glycol and ethanol as solvents and a surface functionalization ligand are mixed and stirred evenly according to certain mole ratio, the evenly-stirred solution is transferred into a hydrothermal kettle for water / solvent heat treatment. After natural cooling, deionized water and ethanol are used for in turn centrifuging, and the obtained precipitate is put into an oven for baking for 6-12 h at 60-120 DEG C under the condition of air to obtain the hydrophilic rare earth nano-material, by use of the one-step water / solvent heat method, the preparation technology is simple, the obtained hydrophilic rare earth nano-material has good stability, high luminous efficiency, adjustable size, controllable morphology, short cycle, low cost, high yield, no toxicity, and no pollution, and can be widely used in security, biological molecular fluorescent tag, biological imaging and other fields.