Disclosed are a multi-layer substrate and a manufacture method thereof. The multi-layer substrate of the present invention comprises a surface dielectric layer and at least one bond pad layer. The surface dielectric layer is located at a surface of the multi-layer substrate. The bond pad layer is embedded in the surface dielectric layer to construct the multi-layer substrate with the surface dielectric layer of the present invention. The manufacture method of the present invention forms at least one bond pad layer on a flat surface of a carrier and then forms the surface dielectric layer to cover the bond pad layer where the bond pad layer is embedded therein. After the multi-layer substrate is separated from the carrier, the bond pad layer and the surface dielectric layer construct a flat surface of the multi-layer substrate.