The present invention relates to a fabricating method of a semiconductor element. First, a substrate is provided and a first layout structure having a first width is formed on the substrate. Then, an etching mask is formed to cover the first layout structure, and the etching mask exposes a portion of the first layout structure. After that, the first layout structure is etched with the etching mask to form a second layout structure having a second width. The second width is less than the first width. This fabricating method is capable of finishing the fabrication of gate structures in two different directions. Accordingly, the layout flexibility is improved.