Herein, we investigated the ethanol-induced structural changes in liposomes over microseconds to tens of seconds using a microfluidic-based SAXS measurement system coupled with molecular dynamics (MD) simulations to provide a plausible detailed structural model of the lamellar structure detected using SAXS. The microfluidic-based SAXS measurement system may capture the structural variations in the liposomes induced by time-dependent changes in ethanol concentration. We confirmed the time-dependent formation of a multilamellar structure and a change in the lipid bilayer distance in the presence of a low concentration of ethanol. MD simulation within 1 μs microscopically complemented the MLV structures at the different ethanol concentrations. Based on both approaches, 50% ethanol was a critical concentration to form liposomes. The combination of time-resolved SAXS and MD simulation enabled us to understand the structural changes in liposomes in detail.