A GaN-based compound semiconductor device includes a GaN-based epitaxial structure and an annealed metal layered structure that is formed on the GaN-based epitaxial structure. The annealed metal layered structure includes a metallic barrier layer, a conductive unit, and a protective unit which is formed on a lateral surface of the conductive unit. The metallic barrier layer and the conductive unit are sequentially disposed on the GaN-based epitaxial structure in such order. An ohmic contact is formed between the GaN-based epitaxial structure and the annealed metal layered structure. The protective unit includes a metal oxide material having one of NiAlO, AuAlO, and a combination thereof.