A method for preparing mesoporous hydroxyapatite nanocrystal includes the following steps: weighing soluble calcium salt and phosphorus pentoxide or phosphate ester at a stoichiometric ratio of Ca/P of 1.67; respectively dissolving the phosphorus pentoxide or phosphate ester into the alcohol solution, and dissolving the soluble calcium salt into the aqueous solution, wherein the volume ratio of the aqueous solution/alcohol solution is of 2/3, 1 or 3/2; mixing the two solutions, adjusting the pH value of the mixed solutino to 9-10 with the ammonia water, and intensively mixing; feeding the solution into a reaction kettle, and carrying out the hydrothermal reaction at a temperature of 140-180 DEG C for 8 hours to obtain hydroxyapatite precipitate; washing with the distilled water, vacuum-filtering; and drying at a temperature of 200DEG C to obtain the mesoporous hydroxyapatite nanocrystal.