This present invention provides a flexible circuit board substrate including: a conductive material layer with a first surface, a second surface opposite to the first surface, and at least one via hole throughout the first surface and the second surface; a first surface-treated layer with a plurality of first particles and a plurality of second particles formed on the first surface and/or the second surface, wherein each first particle has a diameter greater than that of each second particle; and an insulating structure formed on the first surface-treated layer and filled up with the via hole, and a method of manufacturing the same.