A manufacturing method of a substrate structure including vias includes the following steps. A substrate is provided, wherein a material of the substrate includes polyimide. An etching stop layer is formed on the substrate, wherein the etching stop layer covers two opposite surfaces of the substrate. A patterned process is performed on the etching stop layer to form a plurality of openings exposing a part of the substrate. An etching process is performed on the substrate to remove the part of the substrate exposed by the openings and form a plurality of vias.