A method of aligning an upper substrate and a lower substrate is provided. The upper and lower substrates are oppositely arranged, and the aligning method includes the following steps: providing an optical image capturing module; emitting light rays to a third surface of a first prism; filtering the light rays, so that the light rays are divided into light rays at the first wavelength range and light rays at the second wavelength range, wherein the light rays at the first wavelength range irradiate a pattern on the upper substrate, and light rays at the second wavelength range irradiate a pattern on the lower substrate; reflecting a pattern image on the upper substrate to an image capturing apparatus; reflecting a pattern image on the lower substrate to the image capturing apparatus; and determining locations of the patterns of the upper and lower substrate that are on the image capturing apparatus.