A method of manufacturing circuit board structure includes forming a sacrificial layer having first openings on a substrate; forming a metal layer on the sacrificial layer; forming a patterned photoresist layer having second openings over the sacrificial layer, in which the second openings are connected to the first openings and expose a portion of the metal layer; forming a first circuit layer filling the second openings and the first openings; forming a first dielectric layer over the sacrificial layer and covering the metal layer, in which the first dielectric layer has third openings exposing the first circuit layer; forming a second circuit layer filling the third openings and covering a portion of the first dielectric layer; removing the substrate to expose the sacrificial layer, a portion of the metal layer and a portion of the first circuit layer; and removing the sacrificial layer and the metal layer.