The present disclosure provides color filter and a manufacturing method thereof, and a liquid crystal panel with the color filter. The color filter includes a substrate, a black matrix formed on the substrate, a number of spacers integrally formed with the black matrix; and a color filter with a thickness thereof being less than that of the black matrix. Color ink is disposed in the black matrix and is hardened to form the color filter layer. The black matrix and the spacers are integrally formed and made of the black film, which simplifies the manufacturing process of the color filter. Additionally, since the color filter layer is formed by the ink jet printing method, the height of the color filter is unlimited, which allows the black matrix and the spacers to be made of conventional material, and improves the yield rate of the color filter.