The invention is suitable for the circuit board manufacturing technology field and discloses an aluminum-based flexible circuit board manufacturing method. The method comprises steps that a, an aluminum substrate is manufactured, including rough shape cutting, positioning hole drilling, aluminum-based groove milling, groove hole grinding, aluminum-based coarsening, PP rough shape cutting, stitching, PP film pasting and laser cutting; b, a flexible circuit board is manufactured, including rough shape cutting, inner layer film drying, inner layer exposure, inner layer AOI, inner layer graph, target practice, stripping, soft board coarsening, covering film windowing, positioning hole drilling, laser cutting, covering film stitching, browning, gold plating and plasma glue removing; and c, stitching is carried out. According to the method, the aluminum substrate and the flexible circuit board are combined through a prepreg, so the whole aluminum-based flexible circuit board has excellent heat radiation characteristics, electronic components on the aluminum-based flexible circuit board can be prevented from being exposed in the high temperature environment, and service life and reliability are improved.