A gallium nitride (GaN)-based compound semiconductor device having a structure improving a surface characteristic of a thin film growing on a substrate is provided. The GaN-based compound semiconductor device includes an AlxInyGa1−x−yN substrate (0≦x≦1, 0≦y≦1, and 0≦x+y≦1) whose surface inclines toward a predetermined direction at an off-angle of greater than 0° and less than 1° with respect to the (0001) plane, and a GaN-based compound semiconductor layer grown on the surface of the substrate.