Provided is a manufacturing method of a circuit board structure including steps as below. A glass film is provided on an electrostatic chuck (E-chuck). A plurality of first conductive vias are formed in the glass film. A first circuit layer is formed on an upper surface of the glass film, such that the first circuit layer is electrically connected with the first conductive vias. A first polymer layer is formed on the first circuit layer. The first polymer layer covers a surface of the first circuit layer and the upper surface of the glass film. A plurality of second conductive vias are formed in the first polymer layer. A second circuit layer is formed on the first polymer layer, such that the second circuit layer is electrically connected with the second conductive vias. The E-chuck is removed.