A method of fabricating a patterned structure of a semiconductor device is provided. First, a substrate having a first region and a second region is provided. A target layer, a hard mask layer and a first patterned mask layer are then sequentially formed on the substrate. A first etching process is performed by using the first patterned mask layer as an etch mask so that a patterned hard mask layer is therefore formed. Spacers are respectively formed on each sidewall of the patterned hard mask layer. Then, a second patterned mask layer is formed on the substrate. A second etching process is performed to etch the patterned hard mask layer in the second region. After the exposure of the spacers, the patterned hard mask layer is used as an etch mask and an exposed target layer is removed until the exposure of the corresponding substrate.