Four new uranyl triphosphonates, namely, [N-(CH4)(4)] [UO2(H3L)] [H2O] (1), [(UO2)(1.5)(H3L) (H2O)(1.5)] [H2O] (2), [NBu4] [(UO2)(3.5)(H2L)(2)] [(H2O)(4.5)] (3), and [(UO2)(1.5)(H3L)-(H2O)(2.5)] [(H2O)(2.5)] (4), where H6L = benzene-1,3,5-triyltris-(methylene)triphosphonic acid, were obtained from a triphosphonate ligand in the presence of different quaternary ammonium cations. The structural characterization revealed that the introduction of quaternary ammonium cation had a major impact on the structure formation of uranyl phosphonates. Compound 1 possesses a three-dimensional anionic framework structure. Tetramethylammonium cations are accommodated in the channels, serving as counterions and structure directing agents. Compound 2 also displays a three-dimensional framework structure but is neutral, because the tetrapropylammonium cations are not involved in the crystal structure. Compound 3 has an intercalation structure; between the layers are the tetrabutylammonium cations, balancing the charge and strengthening the supramolecular structure with C-H center dot center dot center dot O interactions. No obvious uptake of N-2 and CO2 could be observed for compound 2 due to the shrinkage of the framework and structural transformation. Compound 2 undergoes single-crystal to single-crystal transformation under vacuum, leading to the formation of compound 4, which possesses a two-dimensional layer structure. The photophysical properties of these compounds were also investigated.