An ab initio powder X-ray crystal structure analysis revealed that layered zinc 1,3,5-benzenetriphosphonates containing interlayer tetramethylammonium (ZBP–TMA) or 4,4′-bipyridinium cations (ZBP–bpy) are transformed to novel isomorphous 3D open-framework compounds ZBP–M (M: K, Rb, and Cs) by treatment in aqueous alkali metal chloride solutions. ZBP–Ms have a pillared layer-type of anionic framework containing 2D zigzag channels connected with cage-like spaces. The potassium atoms in ZBP–K are located near 8MR windows in the 2D zigzag channels, and the potassium cations are successfully exchanged with ammonium cations retaining the open-framework structure. The ammonium form (ZBP–NH₄) showed remarkable cation exchange selectivity for Rb⁺ and Cs⁺ in a mixture of alkali metal cations. It is assumed that zinc ions partially dissolved from the starting layered ZBP precursors are intercalated in ZBP layers to form pillared layered 3D open-frameworks. These results clearly show that topotactic pillared layer approaches are applicable not only to zeolite-related materials but also to novel open-framework metal organophosphonates.