A liquid crystal display device, a color filter substrate and a protruding structure, and a manufacturing method thereof are provided. The color filter substrate includes a transparent substrate, a black matrix, a plurality of color filters, a plurality of first protruding structures, and a plurality of second protruding structures. The black matrix is disposed on the transparent substrate and exposes part of the transparent substrate for defining a plurality of first openings, a plurality of second openings, and a plurality of pixel regions, wherein the size of each first opening is different from the size of each second opening. In addition, the color filters are disposed in the pixel regions. The first protruding structures and the second protruding structures are disposed on the transparent substrate, wherein the first protruding structures correspond to the first openings respectively and the second protruding structures correspond to the second openings respectively.