Disclosed is a via structure in a multi-layer substrate, comprising a first metal layer, a dielectric layer and a second metal layer. The first metal layer has an upper surface. The dielectric layer covers the first metal layer in which a via is opened to expose the upper surface. The second metal layer is formed in the via and contacts an upper surface and an inclined wall of the via. A contacting surface of the second metal layer has a top line lower than the upper edge of the inclined wall. Alternatively, the second metal layer can be formed on the dielectric layer as being a metal line simultaneously as formed in the via as being a pad. The metal line and the pad are connected electronically. The aforesaid metal second layer can be formed in the via and on the dielectric layer by a metal lift-off process.