The invention discloses a color filter substrate comprising a substrate, a black matrix layer, a plurality of color filter films and at least a repair structure. The black matrix layer is arranged on the substrate and provided with a plurality of openings; the black matrix layer is provided with at least a defect area positioned between every two adjacent openings; the color filter film is arranged in the opening, and the repair structure is arranged on the defect area; and the repair structure comprises an ink-receptive material layer and an ink-repellent material layer, wherein the ink-receptive material layer is arranged on the substrate, and the ink-receptive material layer contacts with an adjacent color filter film. In addition, the ink-repellent material layer is stacked on the ink-receptive material layer. The invention further provides a manufacture method of the color filter substrate.