A manufacturing method of a color filter comprising the following steps is provided. At first, a transparent substrate is provided. Next, a black matrix is formed on the transparent substrate to define a plurality of pixel areas on the transparent substrate. Then, an isolation layer is formed and patterned on the black matrix and then Red/Green/Blue color filter inks are filled into each of the pixel areas separately by inkjet printing. After that, the color filter inks are dried to form color filter units and optionally the isolation layer can further be patterned to form plenty of photo spacers on the black matrix. The isolation layers prevented the color filter inks from spilling out of the pixel areas and color mixing problems during color filter inkjet fabrication. Besides, it is characterized that the color filter units can be formed with even thickness.