The invention discloses a manufacturing method of a color filter structure. According to the method, transparent photoresists are arranged on a wafer in a coated mode to form a transparent photoresistlayer; a lithography process is executed to form a virtual coating, wherein the virtual coating contains multiple grooves and multiple columnar transparent photoresists, and the grooves are arrangedbetween every two adjacent columnar transparent photoresists; and color filter layers are arranged in the grooves in a coated mode to form the color filter structure.