Study the effect of drugs and biological membranes is of prime importance on understanding drugs’ curative effects and improving their biological properties. In this article, Raman spectrum has been combined with differential thermal scanning technology to discuss the relationship between five categories of ginsenoside molecules and DMPC bilayer films. Raman results indicated that the saponin molecules have not altered the polarity conformation of O—C—C—N+ backbone in DMPC bilayers, and the polarity head still paralleled to the membrane surface. The order of the internal molecular chain and the lateral chain-chain packing have been decreased as the panaxadiol saponins Rb1 and Rh2 increased, and to the opposite, the panaxatriol saponins Re, Rf and Rg1have showed weak effects on DMPC bilayers. The DSC showed further results that the strong effects of ginsenoside Rb1 and Rh2 on DMPC, which both have obviously reduced the DMPC molecular phase transition temperature, thus increasing the fluidity of bilayers. In addition, panaxatriol saponin Rf has displayed stronger disturbance effect on DMPC than Re and Rg1.