The present invention relates to the field of biomaterial preparation, and provides nano-rod-like structure hydroxyapatite and a preparation method thereof. According to the preparation method, calcium lactate is adopted as a calcium source, creatine phosphate is adopted as a phosphorus source, and a hydrothermal reaction is performed to prepare the nano-rod-like structure hydroxyapatite. According to the present invention, the nano-rod-like structure hydroxyapatite has controlled appearance and controlled size, can be used as the biomedical material in the fields of drug delivery, bone defect repair and the like, and has good application prospect; the nano-rod-like structure hydroxyapatite is prepared by using the hydrothermal method, such that the reaction controllability is good; and the preparation process is simple, the operation is convenient, the complicated and expensive equipment is not needed, and the method is expected to achieve the industrial production.