A color filter and a manufacturing method thereof are disclosed. The color filter includes a plurality of first black matrixes and a plurality of second black matrixes disposed on a substrate, and each of the second black matrixes is positioned between adjacent two of the first black matrixes. The first black matrixes define a plurality of sub-pixels, and the second black matrixes are located in the sub-pixels. A plurality of color layers are positioned in the sub-pixels, and portions of the color layers are positioned on the second black matrixes to form a plurality of protrusions.