A method for manufacturing a three-dimensional structure includes forming a first structure having a relief pattern on a substrate, forming a sacrifice layer on the first structure such that the sacrifice layer can be filled in a concave part of the first structure and the sacrifice layer can cover a surface of a convex part of the first structure on a side opposite to the substrate, forming a second structure having a relief pattern on the sacrifice layer, and a fourth step of removing the sacrifice layer from between the first structure and the second structure, and thereby bringing the second structure into contact with the surface of the first structure.