Ion-pair amphiphiles (IPAs, also known as catanionic surfactants) are lipid-like double-chained molecules potentially used for fabricating liposome-like vesicular drug and gene carriers. Frequently ethanol and cholesterol are added to modulate the properties of their bilayer membranes. Effects of ethanol and cholesterol on the fundamental properties of IPA bilayers such as thermotropic phase behavior, however, is not known. In this work, the bilayer phase transition behavior of two IPAs (decyltrimethylammonium-tetradecyl sulfate, DeTMA-TS, and dodecyltrimethylammonium-dodecyl sulfate, DTMA-DS) in tris buffer with various amounts of ethanol was studied by using differential scanning calorimetry (DSC). Effect of cholesterol (CHOL) addition on bilayer phase transition of IPAs with 20 vol% ethanol was thereafter systematically investigated. The experimental results showed that the main phase transition temperature (Tm) was monotonously decreased with the increase of ethanol concentration up to 30 vol%. The degree of Tm depression by ethanol is essentially the same for the two IPAs regardless of different symmetry in the hydrocarbon chains. Further addition of CHOL, however, caused a slight decrease in Tm on the one hand and a significant decrease in the enthalpy of phase transition on the other hand. When the added CHOL exceeded a specific amount, the phase transition disappeared. More hasty disappearance of phase transition was found for IPA with asymmetric structure than the symmetric one. Possible mechanisms of ethanol effect based on binding in the headgroup region of the bilayers and CHOL effect based on opposite (condensing and disordering) interactions with IPA molecules in bilayers, respectively, were proposed.