The hydrogen permeable substrate includes a copper plate, a stainless steel plate, an insulating member, and hydrogen permeable metal. The hydrogen permeable substrate is formed by locating the insulating member between the stainless steel plate and a combined member formed by embedding the hydrogen permeable metal in through-holes made in the copper plate; subjecting the joining face of each component for joining to other components to irradiation with argon ions, to remove the oxide film thereon and activate the surface; and stacking and rolling the components. By so doing, they may be joined at low temperature and low pressure. Once joined, by cutting the hydrogen permeable metal into individual pieces along cut lines, a plurality of hydrogen permeable substrates may be manufactured all at once.