The structure of unilamellar vesicles (ULVs), comprising long- and short-chain lipids, was investigated, and the formation of nanopores on the surface of the ULVs was confirmed under the condition of long- and short-chain lipids being separated. It was also revealed that the behavior of the structural phase transition from ULVs to bilayered micelles (bicelles) depends on the number of nanopores formed on the surface of the ULVs. Because both the rim structures of nanopores and bicelles are considered to be microdomains of short-chain lipids, this phase behavior was explained by considering the kinetic pathway of the growth of the rim domain. It was concluded that the phase segregation of lipids plays an essential role in the rim formation of nanopores as well as bicelles.