Fluorescence emission spectra, FTIR spectra, zeta potential measurements, and ab initio quantum calculation are used to study the interaction between puerarin and membranes composed of egg phosphatidylcholine (PC) liposome. The hydrophobic interactions cause the puerarin molecule to partition into lipid bilayers with its B-ring, and favor the displacement of acid-base equilibrium of puerarin towards the base form. Due to the hydrogen bond formation between the puerarin hydroxyl groups and polar groups of PC molecules on the water/membrane interface, puerarin can easily intercalate into the organized structure of phospholipids and modulate the membrane function. Our results reveal that the liposome membrane integrity is significantly higher compared with that of empty liposome.