This research uses Molecular Dynamics (MD) simulations to explore the structural properties and feed transportation behaviors of Ionic Liquid-Polydimethylsiloxane (IL-PDMS) membranes in the pervaporation (PV) process. The effects of concentration, temperature, and surface area on IL-PDMS membranes and the Fractional Free Volume (FFV) and Mean-Squared Displacement (MSD) are examined. Additionally, the glass transition temperatures (Tg) are explored through the construction of a specialized IL-PDMS unit cell. The simulated Tg value of a pure PDMS is 150 K, which aligns with previous studies, validating the method’s accuracy and highlighting its potential application for investigating the glass transition of various polymers. By analyzing feed movement, including ethanol/water trajectories, MSD, and diffusivity at different temperatures, the diffusion mechanism within the IL-PDMS membrane matrix is elucidated. An increment in the operational temperature enhances the chain mobility of the polymer and enlarges the membrane’s free volume. Notably, water molecules exhibit higher mobility due to their smaller size and less attraction to PDMS, resulting in a small transfer hindrance compared to ethanol. As a result, ethanol demonstrates a greater preference for concentrating within the IL-PDMS membrane from ethanol/water mixtures. The findings demonstrate the efficacy of MD simulations in analyzing the performance of IL-PDMS membranes during pervaporation separation. This approach offers valuable insights into membrane behavior and holds promise for advancing membrane-based processes.