We describe how supramolecular assembly, mediated by control of the ratio of the hetero-atoms in the units [Mo₂S₂O₂]²⁺ and SeO₃²⁻ leads to the formation of new types of building blocks, [(Mo₂O₂S₂)₃(OH)₄(H₂O)₆(SeO₃)] = {Mo₆} and [(Mo₂O₂S₂)₂(OH)₂(H₂O)₄(SeO₃)] = {Mo₄} which are linked in an type of inorganic ‘panelling’ to the assembly of a range of new clusters 1–3 with the general formula {(Mo₂O₂S₂)_x(OH)_y(SeO₃)_z(H₂O)_w}ⁿ⁻, where x, y, z, w, n = [8, 0, 20, 8, 24] for 1, [14, 14, 17, 8, 20] for 2 and [8, 8, 8, 0, 8] for 3. Cluster 1, a rare example of inorganic cryptand, exhibits an elliptical “endo” motif defining an anisotropic ellipse with the dimensions 1.7 × 1.0 nm, with pores ranging from 5.3 to 6.4 Å and site selective cation recognition properties; cluster 2 exhibits an “exo” structural motif constructed by 3 × {Mo₆} and 2 × {Mo₄} panels spanning a cross shape 2.4 × 2.0 nm and cluster 3 a ring shaped structure of a 1.5 nm in diameter. The control of endo vs. exo topology as a function of the Se : Mo ratio is reflected to the difference in surface area of ca. 500 Ų between clusters 1 and 2 intermolecular interactions and proton conduction properties, and this work shows that very simple synthetic parameters can critically change the structure and properties of all-inorganic nanoscale chalcogenide–polyoxometalates.