A method for manufacturing a nitride semiconductor device, comprises: epitaxially growing a semiconductor layer of a GaN-based material on the Ga surface of a GaN substrate while the GaN substrate is mounted on a substrate holder the substrate warping during the epitaxial growth so that a epitaxial deposit is deposited on the N surface of the substrate; and subjecting the N surface of the GaN substrate to vacuum suction after the epitaxial growth of the semiconductor layer; removing the epitaxial deposit from the N side of the GaN substrate after the semiconductor layer has been epitaxially grown, and before the N surface of the n-type GaN substrate is subjected to vacuum suction.