We synthesized lamellar solids by co-condensation of 3-(2-aminoethylamino)propyltriethoxysilane (AeAPTES) and tetraethyl orthosilicate (TEOS) in the presence of hexadecylsuccinic acid (C16SA) and hexadecanol (C16OH) producing a composition in the gel such that AeAPTES : C16SA was kept constant at 1 : 1, as is the ratio of TEOS : C16OH, while the ratio AeAPTES : TEOS was varied from 10 : 0 to 1 : 9. Since a good lamellar solid is obtained only from AeAPTES and C16SA, TEOS and C16OH were expected to be dilutants of AeAPTES and C16SA, respectively, in order to increase the inter-spacings of 3-(2-aminoethylamino)propyl (AeAP) functions in the polysilsesquioxane layer (NH2C2H4NHC3H6SiO1.5)n. All XRD patterns are attributed to lamellar structures with the interlayer distance d = 4.10 ± 0.06 and 2.86 ± 0.10 nm, for the solids 10–0 to 4–6 and the solids 3–7 to 1–9, respectively, where m–n denotes after mixing ratio m : n of AeAPTES : TEOS. Assemblies of alkyl chains in all-trans conformation were revealed by infrared spectroscopy for all of these lamellar solids. The ionization state of –COOH also changed between 4–6 and 3–7, while the amount of nitrogen in the solid continuously decreased with addition of TEOS into the sol. In the sorption of Cu2+ by the lamellar solids and the structural analysis of sorbate by ESR and XAFS, we show that, at the XRD pattern change, the local structure of Cu2+ changes also from [Cu(AeAP)2]2+ to [Cu(AeAP)(H2O)2]2+, which is accompanied by a sudden change in the uptake of Cu2+ as measured by Cu : N ratio, from Cu/N = 0.23 ± 0.03 to Cu/N = 0.43. Since the structure [Cu(AeAP)2]2+ is possible only with short mutual distances of AeAP, these discontinuous changes imply that the enlargement of the spacing between AeAP functions is induced by contraction of the lamellar structure. We further investigated the chemical bond between Cr in chromate and Cu2+ in the above structures by Cr K-edge XANES and EXAFS and demonstrate that the bond is stronger with [Cu(AeAP)2] than with [Cu(AeAP)(H2O)2]. From this result regarding the reactivity of Cu2+, the enlargement of the spacings in the support matrix by a mesostructural transition may become a key concept to provide highly active adsorbents and catalysts with a hierarchical structure.