This invention relates to an ion exchange membrane for a flow-electrode capacitive deionization (FCDi) device, a manufacturing method thereof and a flow-electrode capacitive deionization device including the ion exchange membrane, wherein the ion exchange membrane includes a porous polymer substrate; and a polymer electrolyte incorporated into pores of the porous polymer substrate. According to this invention, a cation exchange membrane and an anion exchange membrane for a flow-electrode capacitive deionization device, having superior ion conductivity, enable ions in feed water such as brackish water to be more rapidly transferred into the pores of the electrode active materials of flow electrodes, thereby remarkably increasing desalination efficiency of the flow-electrode capacitive deionization device, and stable operation of the flow-electrode capacitive deionization device becomes possible because of high water resistance and heat resistance of such ion exchange membranes.