Digitonin is an amphiphilic steroidal saponin, a class of natural products that can bind to cholesterol and lyse cells. Despite the known cell membrane lysis activity, it remains unclear how it interacts with cell membranes. In the present work, the interaction mechanism between digitonin and cell membrane models has quantitatively been investigated using a combination of physical techniques. It has been demonstrated that digitonin molecules bind specifically to cholesterol in the membrane, resulting in the formation of cholesterol-digitonin complexes on the membrane surface by removing cholesterol from the membrane core. Changes in the mass density and the film mechanics caused by the digitonin were determined by using quartz crystal microbalance with dissipation (QCM-D), and the combination of X-ray reflectivity (XRR) and dual polarization interferometry (DPI) yielded the hydration level of the cholesterol-digitonin complexes. From differential scanning calorimetry (DSC) analysis, supporting evidence was obtained that cholesterol was removed from the membrane core.