A circuit board structure and a manufacturing method thereof are provided. The circuit board structure includes a composite substrate, a dielectric layer, and a circuit layer. The composite substrate includes a metal substrate doped with non-metal powders and a metal buffer layer. A surface of the metal buffer layer opposite to the other surface of the metal buffer layer in contact with the metal substrate is treated by a polishing process. The dielectric layer is formed on the polished surface of the metal buffer layer, and the circuit layer is formed on the dielectric layer. Alternatively, a barrier layer is interposed between the dielectric layer and the metal buffer layer for preventing a diffusion effect of the metal buffer layer.