A manufacturing method of a circuit board structure includes the following steps: providing an inner circuit structure which includes a core layer; performing a build-up process to laminate a first build-up circuit structure on a first patterned circuit layer of the inner circuit structure, wherein the first build-up circuit structure includes an inner dielectric layer, and the inner dielectric layer directly covers an upper surface of the core layer and the first patterned circuit layer; removing a portion of the first build-up circuit structure to form an opening extending from a first surface of the first build-up circuit structure relatively far away from the inner circuit structure to a portion of the inner dielectric layer; performing a sandblasting process on a first inner surface of the inner dielectric layer exposed by the opening to at least remove the portion of the inner dielectric layer exposed by the opening.