A manufacturing method of a substrate structure includes the following steps. A first build-up circuit structure is formed. At least one copper pillar is formed on the first build-up circuit structure. A dielectric layer is formed on the first build-up circuit structure, and the dielectric layer wraps the copper pillar. A second build-up circuit structure and a capacitive element are formed on the dielectric layer. In particular, the second build-up circuit structure and the first build-up circuit structure are respectively located at two opposite sides of the dielectric layer. The capacitive element is disposed in a capacitive element setting region within the second build-up circuit structure. The copper pillar penetrates the dielectric layer and is electrically connected to the second build-up circuit structure and the first build-up circuit structure. A substrate structure obtained by the manufacturing method of the substrate structure is provided.