A method for manufacturing a circuit board structure is provided. First, a first circuit layer is formed on a carrier. Then, a first dielectric layer is formed on the carrier and the first circuit layer. Thereafter, at least one first hole is formed in the first dielectric layer to expose a portion of the first circuit layer. Then, a second dielectric layer is formed on the first dielectric layer and the first circuit layer. Thereafter, at least one trench and at least one second hole are formed in the second dielectric layer, in which the trench exposes a portion of the first dielectric layer, and the second hole exposes the portion of the first circuit layer. The second hole is disposed in the first hole. Then, a metal layer is formed to fill the trench and the second hole.