Polyhedral oligomeric silsesquioxanes (POSSs), Am-POSS(x,y), prepared by hydrolytic condensation, contains two types of ammonium side-chain groups, where the numbering of x and y represents the type of ammonium ions in the POSS structure, corresponding to primary (1), secondary (2), tertiary (3), and quaternary (4) ammonium ions. Mixtures of the two starting materials selected from organotrialkoxysilanes containing primary, secondary, and tertiary amines and a quaternary ammonium salt [(RO)3Si(CH2)3R′, R = CH3 or CH2CH3, R′ = NH2, NHCH3, N(CH3)2, and N(CH3)3Cl] were dissolved in dimethyl sulfoxide (DMSO). The hydrolytic condensation was performed in the presence of bis(trifluoromethansulfonyl)imide (HNTf2) and water. All Am-POSS(x,y) structures consisted of a cage-type octamer (T8-POSS), as confirmed by 29Si NMR spectrometry and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Differential scanning calorimetry (DSC) and X-ray diffraction (XRD) analyses indicated that Am-POSS(1,3), Am-POSS(1,4), and Am-POSS(2,4) had amorphous structures. These POSSs have two or three differences in the number of methyl groups between the two types of ammonium side-chains. Conversely, Am-POSS(1,2), Am-POSS(2,3), and Am-POSS(3,4) had crystalline structures. The difference in the number of methyl groups between the two types of ammonium side-chains in these POSSs is only one. Therefore, the crystalline-amorphous structure of Am-POSS(x,y) is controlled by the side-chain group combinations. Furthermore, Am-POSS(1,3), Am-POSS(1,4), and Am-POSS(2,4) are protic ionic liquids with relatively low flow temperatures.