The present invention provides a silicon carbide composite wafer and a manufacturing method thereof. The silicon carbide composite wafer includes (a) a silicon carbide material and (b) a wafer substrate, and the upper surface of the wafer substrate is bonded to the lower surface of the silicon carbide material, wherein the lower surface of the silicon carbide material and/or the upper surface of the wafer substrate undergo a surface modification, thereby allowing the silicon carbide material to be bonded to the wafer substrate directly and firmly. The technical effects of the present invention include achieving strong bonding between the wafer and the substrate, reducing manufacturing process, increasing yield rate, and achieving high industrial applicability.