The invention relates to a surface modified magnesium alloy material as well as a preparation method thereof and an application thereof. The surface of the surface modified magnesium alloy material has a micro-nano composite structure, and comprises a magnesium oxide layer and magnesium-aluminum lamellar double-metal hydroxides, wherein the magnesium oxide layer is generated on the magnesium alloy surface in situ and has micron-sized holes; and the magnesium-aluminum lamellar double-metal hydroxides are generated in the holes of the magnesium oxide layer in situ, and the surfaces of the hydroxides have naono sheet structures. The surface modified magnesium alloy material has excellent corrosion resistance and biocompatibility, and can be widely applied to magnesium alloy medical apparatuses and instruments relevant to bone tissue repair.