A novel method for preparing a fluorine-containing nano-hydroxyapatite coating on the surface of a biomedical magnesium alloy comprises the following steps that (1) a cleaned pure magnesium or magnesium alloy substrate material is immersed into 20-40wt% of hydrofluoric acid for 18-30 h, then cleaned in deionized water and dried; (2) an electrolyte is prepared, the concentration of Ca<2+> in the electrolyte is 10.5 mmol/L-42 mmol/L, the concentration of H2PO4<-> in the electrolyte is 6.3 mmol/L-25 mmol/L, the Ca/P molar ratio is 1.6-2.0, the concentration of NaNO3 in the electrolyte is 0.058 mol/L-0.117 mol/L, and the pH value of the electrolyte is adjusted to be 4.5-5.5 for standby application; and (3) the pure magnesium or magnesium alloy substrate material treated in the step (1) servingas a cathode and a graphite electrode serving as an anode are put into the electrolyte in the step (2), hydroxyapatite is deposited on the surface of the fluorinated substrate material through a dipulse electrodeposition method, and thus the fluorine-containing nano-hydroxyapatite coating is obtained.