A method for manufacturing a substrate structure is provided. The method includes the following steps. A substrate is provided. The substrate has a patterned first metal layer, a pattern second metal layer and a through hole. After that, a first dielectric layer and a second dielectric layer are formed at a first surface and a second surface of the substrate, respectively. The second surface is opposite to the first surface. Then, the first dielectric layer and the second dielectric layer are patterned. After that, a first trace layer is formed at a surface of the patterned first dielectric layer. The first trace layer is embedded into the patterned first dielectric layer and is coplanar with the first dielectric layer. Then, a second trace layer is formed on a surface of the second dielectric layer.