The present invention provides a color filter and a manufacturing method thereof. The method includes steps of: coating a first material layer on a substrate and patterning it to have first photoresists, first filter portions and first spacer portions; coating a second material layer on the substrate and patterning it to have second photoresists, second filter portions and second spacer portions; and coating a third material layer on the substrate and patterning it to have third photoresists, third filter portions and third spacer portions; and the first, the second, the third filter portions are correspondingly overlapped with each other, and the first, the second, the third spacer portions are correspondingly overlapped with each other.