A substance separation structure comprises a base material including a porous material having a continuous hole with an opening of the hole formed on at least one surface, a porous layer, formed to fill up the opening, having a hole smaller than the hole of the base material and a permeable membrane of not more than 1 &mgr;m in thickness formed on at least one surface of the base material formed with the porous layer to selectively permeate ions or neutral elements or molecules, and the surface roughness of at least one surface of the base material formed with the porous layer is not more than 0.3 &mgr;m in Rmax. The surface of the base material is polished with abrasive grains containing a porous material so that the opening of the base material can be filled up with the porous layer, and the permeable membrane is formed by ion plating.