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 dicing process is performed, such that at least one slit is formed in the glass film. A plurality of first conductive vias are formed in the glass film. A first circuit layer is formed on the glass film. A polymer layer is formed on the first circuit layer. The polymer layer covers surfaces of the first circuit layer and the glass film. A plurality of second conductive vias are formed in the polymer layer. A second circuit layer is formed on the polymer layer, such that a first circuit board structure is formed. A singulation process is performed, such that the first circuit board structure is divided into a plurality of second circuit board structures.