A method for forming a self-aligned overlay mark is disclosed. First, a first region, a second region and a main feature which is disposed between the first region and the second region all disposed on the substrate are provided. The first region defines a first edge and the second region defines a second edge. Second, a cut mask layer is formed to respectively cover the first region and the second region to expose the main feature. Next, the cut mask layer is determined if it is self-aligned with the second edge or the first edge, and creates a self-aligned overlay mark. Later, a main feature etching step is carried out to transfer the main feature into the substrate when the cut mask layer is determined to be self-aligned with the second edge or the first edge.