Disclosed is a flexible printed circuit board with waterproof structure, including a flexible substrate that has a first surface on which a first metal layer is bonded. The first metal layer has an upper surface forming a covered area and at least one mounting zone and the metal layer forms on a surface thereof within the mounting zone a bonding improved waterproof structure. A first insulation layer is formed on the covered area of the upper surface of the first metal layer in such a way not to cover the mounting zone of the first metal so as to expose the mounting zone. A water resistant member is securely mounted to the mounting zone of the first metal layer. The flexible substrate also has a second surface to which a second metal layer and a second insulation layer are mounted. The second metal layer also forms a mounting zone, which is not covered by the second insulation layer so as to expose for mounting the water resistant member. The metal surface inside the mounting zone also forms bonding improved waterproof structure. The waterproof structure improves the bonding strength between the flexible printed circuit board and the water resistant member through proper arrangement and selection of shape, size, and distribution density of holes that are defined in the exposed metal surface. Alternatively, the holes can be made completely through the metal layer in order to also feature control of impedance for high frequency signals.