A method for manufacturing flexible color filter substrate includes the following steps. First, a rigid substrate is provided. The rigid substrate has an upper surface and a lower surface opposite to the upper surface. The upper surface includes a first region and a second region located at a periphery of the first region. Next, a release layer is formed on the first region. Next, a flexible substrate layer is formed to cover the second region and the release layer. Next, a color photoresist layer is formed on a portion of the flexible substrate layer above the release layer. Next, the rigid substrate and the flexible substrate layer are cut along a border between the first region and the second region. Next, the flexible substrate layer is separated with the release layer. The method for manufacturing flexible color filter substrate can improve optical performance of the flexible color filter substrate.