The present invention provides a flexible substrate and a manufacturing method thereof. The flexible substrate is divided into a first organic material layer (21) and a second organic material layer (22). A coverage area of the second organic material layer (22) on a carrying plate (1) is greater than a coverage area of the first organic material layer (21) on the carrying plate (1) and a major, long edge of the second organic material layer (22) encloses a major, long edge of the first organic material layer (21) so as to help reduce the thickness of an edge of the flexible substrate and prevent etching residue at an edge, reduce the coverage area of the organic materials on the carrying plate, and reduce warpage of the flexible substrate. Further, an alignment mark (3) is formed on the second organic material layer (22) at a location between the major, long edge of the first organic material layer (21) and the major, long edge of the second organic material layer (22) to ensure alignment accuracy in subsequent processes, such as vapor deposition. Further, since there is only one layer of organic material at the site of alignment mark (3), light transmission rate is increased and the rate of successful alignment is enhanced.