The present invention provides a Group III nitride crystal substrate whose surface has concavities and convexities reduced in size. The surfaces with concavities and convexities, such as hillocks, pits and facets, of Group III nitride crystals are brought into contact with a melt and thereby the surfaces are subjected to meltback etching or mechanochemical polishing. The melt includes at least one of alkali metal and alkaline-earth metal. Thus a Group III nitride crystal substrate that has reduced strain and a reduced number of defects, which are caused through the processing, and is excellent in surface flatness is manufactured. Furthermore, by the use of the Group III nitride crystal substrate of the present invention, for instance, semiconductor devices of high performance can be obtained.