In this study, a single cyclic tetrasiloxane containing propylammonium trifluoromethanesulfonate and methyl side-chain groups (Am-CyTS) was selectively prepared by the hydrolytic condensation of 3-aminopropyldiethoxymethylsilane using aqueous superacid trifluoromethanesulfonic acid. The (1)H NMR spectrum of Am-CyTS in D2O exhibited a single signal assigned to a methyl group, and the (29)Si NMR spectrum of Am-CyTS in DMSO-d6 also exhibited only one signal. In the matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and the electrospray ionization mass spectrometry (ESI MS) analyses, the peaks corresponding to the masses of the cyclic tetrasiloxane were observed. These results indicate that Am-CyTS is a single cyclic tetrasiloxane without isomers. In addition, the result of a single-crystal X-ray structural analysis of its tert-butoxycarbonyl (Boc)-protected compound (Boc-CyTS) indicated the formation of a cis-trans-cis cyclic tetrasiloxane forming two-dimensional layered aggregates. Moreover, it was found that two-dimensional layered aggregates could be formed by drop-casting an aqueous solution of Am-CyTS and chloroform solution of Boc-CyTS onto glass substrates, as shown by powder X-ray diffraction measurements.