Ionic liquids (ILs) have proved to be efficient catalysts for the alcoholysis of poly(ethylene terephthalate) (PET). However, the in-depth understanding about the alcoholysis of PET at a molecular level remains scarce. Herein, the microstructures and dynamics of ILs/methanol systems with and without PET oligomer were investigated using molecular dynamics (MD) simulations. A better miscibility between [OAc]-containing ILs and methanol is observed. There exist hydrogen-bonding networks between cation, anion, and methanol, in which the cation serves as a donor and methanol as an acceptor, while the anion/methanol hydrogen-bonding interaction follows the opposite donor–acceptor relationship. In ILs/methanol/PET ternary systems, the hydroxyl groups of [Cho] cations display a more significant interaction with carbonyl groups of PET oligomer than [Emim] cations. In addition, PET oligomer diffuses quite faster in [Cho][OAc] compared to [Emim][OAc]. The information obtained in this work is helpful to better understand the mechanism of the PET alcoholysis process.