A method of manufacturing a color filter substrate is provided. The color filter substrate includes a substrate, a light-shielding layer, and a plurality of color filter patterns. The substrate has a plurality of annular trough areas, a plurality of central areas, and a light-shielding area positioned among the annular trough areas. Each of the annular trough areas has an inner edge connected to the central area and an outer edge connected to the light-shielding area. The light-shielding layer is disposed on the light-shielding area and extends from the outer edges of the annular trough areas to the top of the annular trough areas. The color filter patterns are disposed on the annular trough areas and the central areas, and the color filter patterns are in contact with a side surface and a part of the bottom surface of the light-shielding layer.