The present invention provides a manufacture method of the color filter, comprising: sequentially deposing a metal layer and a black matrix layer on a substrate; implementing a patterning process to the black matrix layer with a half tone mask; removing the metal layer in the color filter area and the black matrix layer in the through hole area; coating a RGB color filter layer in the color filter area; deposing a transparent metal layer on the substrate to form a transparent electrode. The present invention improves the display quality of the liquid crystal display panels.