A color filter substrate including a substrate, a black matrix layer and a color filter substrate layer is provided. The substrate has a plurality of grooves. The black matrix layer is disposed on the substrate between each two adjacent grooves, wherein the black matrix layer extends to the region above the groove from the edge of the groove and an undercut profile forms between the bottom of black matrix and the substrate. The color filter layer including a plurality of filter films separated is filled in the plurality of grooves and the plurality of filter films is separated from each other by the black matrix layer. In addition, a method of fabricating a color filter substrate is also provided. The above-mentioned color filter substrate and the fabricating method thereof can improve the quality and color uniformity of the color filter substrate.