A nitride semiconductor substrate having a rugged surface being lapped by whetting granules to roughness between Rms5 nm and Rms200 nm, which has a function of reducing dislocations of a GaN, InGaN or AlGaN layer epitaxially grown on the lapped substrate by gathering dislocations in the epi-layer to boundaries of holes, pulling the dislocations to bottoms of the holes. Higher roughness of the nitride substrate degrades morphology of an epitaxially-grown layer thereon but reduces dislocation density to a lower level. Morphology of the epi-layer contradicts the dislocation density of the epi-layer. The nitride semiconductor substrate can reduce dislocation density and can be low cost and useful substrates.