The invention relates to a selenium-doped hydroxyapatite and a preparation method thereof. The selenium-doped hydroxyapatite provided is a single crystal comprising a rod-like structure, a uniform morphology, and a good dispersibility. The preparation method comprises adding a mixed solution of a phosphate and a selenite dropwise to a mixed solution of a calcium salt and a dispersing agent, and reacting for 1.5-2.5 hrs at a controlled temperature of 80-90° C., to obtain a solution of a calcium phosphate amorphous precursor, followed by performing a hydrothermal reaction at 190-210° C., to obtain a selenium-doped hydroxyapatite comprising a rod-like structure. Compared with selenium-doped hydroxyapatite with severe agglomeration, the selenium-doped hydroxyapatite provided in the present invention comprises good dispersibility and able to have better prevention of clogging problem in human body when in use, thus having a good prospect using as a multi-functional new material for bone repair in patients as a repair material for bone defects, an anti-tumor, etc.