In a manufacturing method of an opening structure, a multi-layer structure including alternately stacked conductive layers and first dielectric layers is formed on a substrate. The conductive layers in a first region are lower than those in a second region. A second dielectric layer covering the multi-layer structure is formed. A patterned mask layer is formed on the second dielectric layer. A first filling layer covering the second dielectric layer exposed by the patterned mask layer is formed in the second region. First openings exposing the conductive layers in the first region are formed by using the first filling layer and the patterned mask layer as a mask. The first filling layer is removed. A second filling layer filling the first openings is formed. Second openings exposing the conductive layers in the second region are formed by using the second filling layer and the patterned mask layer as a mask.