This paper describes the preparation of a cell-sized vesicle containing small vesicles from a two-planar lipid bilayer in a triple-well device using a pulsed jet flow. First, the size distribution of the cell-sized vesicles is estimated using a double-well device wherein a separator having a hole diameter of 100, 200, or 500 μm is mounted between the wells. Moreover, the small vesicles are successfully formed and immediately encapsulated into a cell-sized vesicle using a triple-well device in which different-sized hole separators are mounted between the wells. We also observed the diffusion of small vesicles in a cell-sized vesicle. This cell-sized vesicle containing small vesicles will create new opportunities for the development of an artificial cell research model, such as intracellular traffic of small vesicles diffusion and fusion.