Disclosed is a manufacturing method of metal structure in multi-layer substrate. The manufacturing method includes following steps: coating at least one photoresist layer on a surface of a dielectric layer; exposing the photoresist dielectric layer to define a predetermined position of the metal structure; removing the photoresist layer at the predetermined position to undercut an edge of the photoresist layer adjacent to the predetermined position by a horizontal distance of at least 0.1 μm between a top and a bottom of the edge; forming the metal structure at the predetermined position; and forming at least one top-cover metal layer to cover a top surface and two side surfaces of the metal structure. The present invention can form a cover metal layer covering the top surface and the two side surfaces by one single photomask.