There is provided a method for manufacturing a nitride semiconductor substrate, comprising: etching and flattening a surface of a nitride semiconductor substrate disposed facing a surface plate, by using the surface plate having a surface composed of any one of Ni, Ti, Cr, W, and Mo or nitride of any one of them, disposing the surface of the surface plate and a flattening surface of a nitride semiconductor substrate proximately so as to be faced each other, and supplying gas containing at least hydrogen and ammonia between the surface of the surface plate and the surface of the nitride semiconductor substrate, wherein the surface plate and the nitride semiconductor substrate facing each other are set in a high temperature state of 900° C. or more.