A method of manufacturing nitride semiconductor substrate, comprising: providing silicon-on-insulator substrate which comprises an underlying silicon layer, a buried silicon dioxide layer and a top silicon layer; forming a first nitride semiconductor layer on the top silicon layer; forming, in the first nitride semiconductor layer, a plurality of notches which expose the top silicon layer; removing the top silicon layer and forming a plurality of protrusions and a plurality of recesses on an upper surface of the buried silicon dioxide layer, wherein each of the plurality of protrusions is in contact with the first nitride semiconductor layer, and there is a gap between each of the plurality of recesses and the first nitride semiconductor layer; and epitaxially growing a second nitride semiconductor layer on the first nitride semiconductor layer, such that the first nitride semiconductor layer and the second nitride semiconductor layer form a nitride semiconductor substrate.