Three novel polyfluorinated cationic surfactants having a short perfluoroacyl group and double long alkyl chains, and three corresponding hydrocarbon analogues were synthesized. All of the surfactants formed small unilamellar vesicles in water upon sonication. The temperature conditions for the sonication were carefully determined by confirming that the DSC curve had a reproducible single phase transition peak. The TEM images indicated that the size of the polyfluorinated vesicles was in the range of 56–89 nm. The NMR relaxation study upon the addition of paramagnetic Mn2+ ions to the bulk water phase showed that the terminal trifluoromethyl group of the short acylamide chain in the surfactants faced directly to the bulk water phase; the vesicle had a unique micro-structure with the perfluoroalkyl group extending its arm straightforwardly to the water phase. The vesicles were named "‘surface polyfluorinated vesicles’'. The local oxygen concentrations surrounding each fluorine nucleus and proton of the surfactants within the vesicles were estimated by observing the longitudinal relaxation time under nitrogen and oxygen atmospheres. Oxygen was enriched in the microenvironment surrounding the long alkyl chain and perfluoralkyl group, while the N-methyl group had a low oxygen concentration around it. The micro-distribution of water within the vesicle was discussed by the estimated local concentration of oxygen. The vesicles were thought to be stabilized by the channel-like water connecting the bulk water phase with the hydrated water of the N-methyl groups inside the vesicles. The surface polyfluorinated layer exhibited a substantial protective effect against the oxidative attack of hydroxyl radical generated in the bulk phase water.