In this study, we investigated the effects of time-dependent changes in ethanol concentration on the structural changes in liposomes using time-resolved SAXS and MD simulations. The microfluidic-based SAXS measurement system could capture ethanol-induced time-dependent structural changes in liposomes. Using SAXS, we observed the structural changes in the liposomes from uni-to multilamellar within 0.8 s of contact with ethanol, and the d-spacing decreased from 6.1 (w/o ethanol) to 4.4 nm (80% ethanol) with increasing ethanol concentration. We also performed MD simulations to understand the structural changes in liposomes with ethanol over a shorter time. The MD simulations revealed that the changes in the lamellar structure caused by ethanol at the molecular level could explain the structural changes in the liposomes observed using time-resolved SAXS.