A color filter and a manufacturing method thereof are provided. In the method of the invention, a substrate having a display area and a non-display area is provided. Thereafter, a black matrix is formed over the substrate, wherein black matrix defines the display area into a plurality of sub-pixel areas, and covers the non-display area, which forms an edge of the display area. Then, a color filter unit is formed in each sub-pixel area, and a light shielding layer is formed over the black matrix simultaneously. Accordingly, the shielding layer of the color filter provided by the present invention is capable of effectively reducing the light leakage from the edge of the display area.