Provided is a method of manufacturing a substrate including an alignment mark, including: forming the alignment mark and a recess portion on the substrate, the alignment mark not penetrating the substrate and including a bottom portion with a lower infrared transmittance than that of a first surface and a second surface of the substrate; and aligning the substrate by orthogonally arranging predetermined positions of the first surface and the second surface of the substrate in a horizontal direction and an infrared ray camera and by image-identifying the alignment mark formed on the substrate with transmitted light of infrared rays emitted from the infrared ray camera.