The invention discloses a color filter manufactured by an ink jet process and a manufacturing method thereof. The color filter comprises a substrate, a plurality of pixel regions positioned on the surface of the substrate, and a plurality of color photoresists. Each pixel region comprises a plurality of sub pixel regions, and the color photoresists are arranged in the sub pixel regions correspondingly. The color photoresists comprise a plurality of hydrophilic photoresists and a plurality of hydrophobic photoresists, wherein the hydrophilic photoresists and the hydrophobic photoresists are arranged in an alternating mode to avoid the overflowing of the color photoresists.