Transfersomes (TRS) can provide sustained drug delivery and themselves are biocompatible, biodegradable and nontoxic. Edge activators (EAs) are key factors for increasing the deformability of TRS, and this active deformation mechanism is of commercial interest, especially at the molecular level. Accordingly, in this paper, the deformability of pure dipalmitoyl phosphatidylcholine (DPPC) vesicles, TRS with sodium cholate as an EA, and DPPC vesicles containing pogostone (POG) were compared via umbrella sampling technology. The DPPC conformation and membrane fluidity of these three types of bilayer systems were evaluated, and the changes in the membrane properties of vesicles caused by EAs were studied. EAs could increase the deformability of TRS by decreasing the deformation energy barrier due to their amphiphilic structures, which was similar to those of DPPC molecules. The membrane properties also changed via treatment with EAs including altering the tail chain angle, disturbing the ordered tail chain arrangement and prompting lateral diffusion of DPPC molecules. In addition, the impact of EAs on DPPC bilayers was further demonstrated to be concentration dependent. An ideal concentration was identified for the lowest amount of EA that offered a gel-liquid-crystalline phase transition of DPPC bilayers. Importantly, POG, a lipophobic transdermal drug, can also affect the skin permeation behavior of vesicles but had weaker effects than EA.