A manufacturing method of substrate structure is provided. A base material having a core layer, a first patterned copper layer, a second patterned copper layer and at least one conductive via is provided. The first and second patterned copper layers are respectively located on a first surface and a second surface of the core layer. The conductive via passes through the core layer and connects the first and second patterned copper layers. A first and a second solder mask layers are respectively formed on the first and second surfaces. Portions of the first and second patterned copper layers are exposed by the first and second solder mask layers, respectively. A first gold layer is formed on the first and second patterned copper layers exposed by the first and second solder mask layers. A nickel layer and a second gold layer are successively formed on the first gold layer.