A pore-filled ion exchange polyelectrolyte composite membrane from which the surface ion exchange polyelectrolyte has been removed and a method of manufacturing the same are provided. The ion exchange polyelectrolyte composite membrane exhibits low film resistance and low in-plane-direction swelling degree, and has a smaller film-thickness than a commercial film, and thus, can be used for various purposes. In addition, since the pore-filled ion exchange polyelectrolyte composite membrane is continuously manufactured through a roll-to-roll process, the manufacturing process is simple, and manufacturing costs can be greatly reduced.