A manufacturing method of substrate structure is provided. The base material having a core layer and a first and second copper foil layers located at a first and second surfaces of the core layer is provided. A surface treatment is performed on the first and second copper foil layers so as to form a first and second roughened surfaces. A laser beam is irradiated on the first roughened surface so as to form at least one first blind hole extending from the first copper foil layer to the second surface. An etching process is performed on the second copper foil layer so as to form at least one second blind hole extending from the second copper foil layer to the second surface. A conductive layer fills up a through hole defined by the first and second blind holes and covers the first and second copper foil layers.