The invention relates to a method for manufacturing color filters utilizing a color electrodeposition coating which contains an anionic electrodeposition resin having a low acid value. Said method comprises coating a layer of positive photoresist onto a transparent electrically conductive substrate, exposing the substrate under a photomask or photomasks to form regions of different initial levels of exposure energy, exposing the entire surface of the substrate through an energy-incrementing way to, progressively, allow all regions of the substrate to achieve an energy sufficient to completely expose the photoresist on each corresponding region, developing stepwise each region with a same developer solution to cause the electrically conductive substrate of the corresponding region uncovered, electrodepositing said region with a color electrodeposition coating containing an anionic electrodeposition resin having a low acid value to finish the pixel arrangements of the desired colors and completely exposing the substrate. The low acid value anionic electrodeposition resin utilized in the invention has an acid value of 1 to 70 mg KOH/g. The method of the invention shows the advantages of having a high degree of freedom in pattern figures and a wide process window. Moreover, the manufacture color filters of large surface and the perfect yield rate of products are possible.