The nature of carboxylic acid has a profound effect on constructing POM-based architectures. With different carboxylic acid ligands, three novel diphosphonate-containing compounds have been synthesized and further investigated by elemental analyses, single-crystal X-ray diffraction, IR spectra, UV-vis spectra, X-ray powder diffraction (XRPD), 31P NMR spectroscopy, cyclic voltammetric behavior and thermogravimetric(TG) analyses. [(HO3PCH2PO3)Mo6O18(O2CC6H4OH)2]5− (1a) shows a ring-shaped cluster with a {Mo6} plane framework. [{(HO3PCH2PO3)Mo6O18(CH3CO2)2}2Na2(H2O)2]8− (2a) is a reverse symmetrical “crown-type” structure and the subunits are linked by two Na–O(1W)–Na bridges. The polyanion [{(O3PCH2PO3)(Mo6O18(H2O)2)(O2CCH2CO2)}2(Mo2O5)2(μ3-O)2]12− (3a) appears an “S-shaped” structure with a centre of inversion.