The invention discloses a preparation method of structurally-controllable hydroxyapatite micro-spheres, and relates to preparation of hydroxyapatite micro-spheres by adjusting the pH value of a solution by using a slightly soluble crystallization principle. The preparation method comprises the following steps: putting nano hydroxyapatite powder prepared by a chemical method into a NaOAc buffer solution with the pH value of 4.9-5.27; stirring for 1 hour by using a magnetic stirrer; adding a certain amount of sodium fluoride solution; stirring for 24 hours by using the magnetic stirrer; filtering a generated white deposit by using distilled water and absolute ethyl alcohol; and then drying in a 75 DEG C environment, thereby preparing the hydroxyapatite micro-spheres. The preparation method is simple in process equipment, convenient in operation and easy for realization of industrial production, and the generated hydroxyapatite micro-spheres is controllable in shape and stable in size.