A method of manufacturing a nitride semiconductor substrate includes providing a silicon substrate having a first surface and a second surface opposing each other, growing a nitride template on the first surface of the silicon substrate in a first growth chamber, in which a silicon compound layer is formed on the second surface of the silicon substrate in a growth process of the nitride template, removing the silicon compound layer from the second surface of the silicon substrate, growing a group III nitride single crystal on the nitride template in a second growth chamber, and removing the silicon substrate from the second growth chamber.