A method for fabricating a color filter layer, which is applied to an integrated circuit manufacturing process, includes the following steps. Firstly, a substrate is provided, and a groove structure is formed on the substrate. The groove structure includes a plurality of positive photoresist patterns and a plurality of trenches. Then, a first group of color filter patterns is formed in the trenches. The plurality of positive photoresist patterns is removed, so that a portion of a top surface of the substrate is exposed. Then, a second group of color filter patterns is formed on the exposed top surface of the substrate.