A method for manufacturing a multi-layer structure is provided. The method includes following steps. First, a stack of alternate conductive layers and insulating layers is formed on a substrate, and the stack includes a multi-layer area and a contact area adjacent to the multi-layer area. Next, a plurality of first openings are formed in the contact area. Then, a conductive connecting structure is formed on the stack and into the first openings. Thereafter, the stack is patterned. The conductive connecting structure continuously extends on the contact area and into the first openings to maintain an electrical connection among the conductive layers while the stack is patterned.