The invention relates to a magnesium-based hydrogen storage alloy with a superlong cycle ordered structure. The chemical molecular formula is Mg-aX-bY, wherein X represents one of Ni, Al, V, Co and Pt; a and b represent mass percentage, a is greater than or equal to 6.52 percent and less than or equal to 13.53 percent, and b is greater than or equal to 20.41 percent and less than or equal to 21.50 percent; the balance is Mg. The preparation method of the magnesium-based hydrogen storage alloy manly comprises the following steps: charging the alloy particles with the components into an induction melting furnace, melting under the atmosphere of argon, pretreating the surface of the melted magnesium-based alloy, abrading, polishing and cleaning, wrapping with a boron nitride tube, putting into a high-pressure six-side top hydraulic machine to press under high pressure of 3 to 4 GPa, heating to 800 to 1300 DEG C, and preserving heat for 30 to 60 minutes to obtain the magnesium-based hydrogen storage alloy with the superlong cycle ordered structure. The process equipment is simple, easy to control and low in cost; compared with the magnesium-based alloy of the common process, the prepared magnesium-based hydrogen storage alloy is lower in hydrogen absorbing and discharging temperature and higher in hydrogen absorbing and discharging dynamic performance.