The invention relates to a method for preparing ellipsoidal ion-doped hydroxyapatite microspheres with porous surfaces. According to the method disclosed by the invention, ellipsoidal hydroxyapatite microspheres are prepared from ellipsoidal calcium carbonate microspheres as a precursor and the support of a plurality of trace ions (Mg, Sr, Zn, Ag, Fe, Si, Y, F, Cl and the like) and fluorescent ion (Eu) is achieved. No surfactant is used in the preparation process of ellipsoidal hydroxyapatite microspheres and ellipsoidal calcium carbonate microspheres, and the sizes of the obtained ellipsoidal hydroxyapatite microspheres and ellipsoidal calcium carbonate microspheres are uniform and the obtained ellipsoidal ion-doped hydroxyapatite microspheres have the characteristics of relatively high specific surface area, fluorescent tracing and bacteriostasis and other properties and are capable of adsorbing positively charged polymers. The hollow or solid ellipsoidal ion-doped hydroxyapatite microspheres prepared by the method disclosed by the invention can be applied as a drug carrier material, a bone repair material, an environmental water treatment material, food or cosmetics additives and the like.