Ionic liquids (ILs) have presented excellent behaviors in the separation of azeotropes in extractive distillation. However, the intrinsic molecular nature of ILs in the separation of azeotropic systems is not clear. In this paper, Fourier-transform infrared spectroscopy (FTIR) and theoretical calculations were applied to screen the microstructures of ethyl propionate–n-propanol–1-ethyl-3-methylimidzolium acetate ([EMIM][OAC]) systems before and after azeotropy breaking. A detailed vibrational analysis was carried out on thev(C=O) region of ethyl propionate andv(O–D) region of n-propanol-d1. Different species, including multiple sizes of propanol and ethyl propionate self-aggregators, ethyl propionate–n-propanol interaction complexes, and different IL–n-propanol interaction complexes, were identified using excess spectroscopy and confirmed with theoretical calculations. Their changes in relative amounts were also observed. The hydrogen bond between n-propanol and ethyl propionate/[EMIM][OAC] was detected, and the interaction properties were also revealed. Overall, the intrinsic molecular nature of the azeotropy breaking was clear. First, the interactions between [EMIM][OAC] and n-propanol were stronger than those between [EMIM][OAC] and ethyl propionate, which influenced the relative volatilities of the two components in the system. Second, the interactions between n-propanol and [EMIM][OAC] were stronger than those between n-propanol and ethyl propionate. Hence, adding [EMIM][OAC] could break apart the ethyl propionate–n-propanol complex (causing the azeotropy in the studied system). Whenx([EMIM][OAC]) was lower than 0.04, the azeotropy still existed mainly because the low IL could not destroy the whole ethyl propionate–n-propanol interaction complex. Atx(IL) > 0.04, the whole ethyl propionate–n-propanol complex was destroyed, and the azeotropy disappeared.