The invention provides a method for preparing a bone filling material by doping lithium citrate into hydroxyapatite nanoparticles, relates to the field of medicines, and aims to solve the problems that a calcium phosphate bone filling material is poor in effects of improving the activity of osteoblasts and inhibiting osteoclast absorption. Lithium chloride is added into hydroxyapatite citrate to form lithium citrate hydroxyapatite. The activity of the osteoblasts is improved, osteoclast absorption is inhibited, and differentiation of mesenchymal stem cells into the osteoblasts is improved, sothat the induced osteogenesis performance of hydroxyapatite serving as the bone filling material is improved. The method is applied to the field of bone materials.