A surface finish structure of multi-layer substrate and manufacturing method thereof. The surface finish structure of the present invention includes a bond pad layer, at least one cover metal layer and a solder mask. The cover metal layer covers the bond pad layer. The solder mask has a hole to expose the cover metal layer. The present invention can form the cover metal layer to cover the bond pad layer and then forms the solder mask. Thereafter, the hole is made to the solder mask at the position of the cover metal layer to expose thereof. Because the bond pad layer is embedded in a dielectric layer of the multi-layer substrate, adhesion intensity between the bond pad layer and the dielectric layer can be enhanced. Meanwhile, contact of the bond pad layer with the solder can be prevented with the cover metal layer.