A manufacturing method of a patterned structure of a semiconductor device includes following steps. A plurality of support features are formed on a substrate. A first conformal spacer layer is formed on the support features and a surface of the substrate, a second conformal spacer layer is formed on the first conformal spacer layer, and a covering layer is formed on the second conformal spacer layer. A gap between the support features is filled with the first conformal spacer layer, the second conformal spacer layer, and the covering layer. A first process is performed to remove a part of the covering layer, the second conformal spacer layer, and the first conformal spacer layer. A second process is performed to remove the support features or the first conformal spacer layer between the support feature and the second conformal spacer layer to expose a part of the surface of the substrate.