The microfluidic-based SAXS system enables the measurement of changes in liposome structure within 0.8 s by increasing the flow rates of the solutions. However, obtaining SAXS data with a high S/N is challenging due to the small number of multilamellar liposomes under these measurement conditions, the small sizes of the liposomes and numbers of multilamellar layers, and the intensity of the X-ray beam. Furthermore, the high flow condition affects the ethanol concentration profile within the microchannel. To further understand the effects of ethanol on the changes in the liposome structures, we performed an MD simulation of the lamellar structure based on the results of SAXS.