There is provided a method for manufacturing a nitride crystal substrate, including: arranging a plurality of seed crystal substrates made of a nitride crystal in a planar appearance, so that their main surfaces are parallel to each other and their lateral surfaces are in contact with each other; growing a first crystal film using a vapor-phase growth method on a surface of the plurality of seed crystal substrates arranged in the planar appearance, and preparing a combined substrate formed by combining the adjacent seed crystal substrates each other by the first crystal film; growing a second crystal film using a liquid-phase growth method on a main surface of the combined substrate so as to be embedded in a groove that exists at a combined part of the seed crystal substrates, and preparing a substrate for crystal growth having a smoothened main surface; and growing a third crystal film using the vapor-phase growth method, on the smoothed main surface of the substrate for crystal growth.