A vesicle is a compartment composed of lipid bilayer of amphiphilic molecules. The vesicle is applied to carriers of drugs, cosmetics and functional food ingredients in industries. Vesicles are also applied as a model for artificial cell membrane and expected as micro- and nano-reactors. They are generally prepared by the hydration of dry lipid film, but there is no method to prepare vesicles of a controlled size and high entrapment yield of hydrophilic materials inside them. In this article, a microchannel (MC) emulsification method was applied to prepare vesicles aimed at controlling the size and improving the entrapment yield. Firstly, monodisperse water-in-oil (W/O) emulsions were prepared by the MC emulsification method. In this process, hydrophilic materials to be entrapped were contained inside the water droplets of the emulsions. Keeping the water droplets frozen, the emulsifier was replaced by a bilayer-forming lipid mixture, and then the oil phase was evaporated. After hydration of lipid layers surrounding the water droplets, vesicles were formed. We call this preparation "lipid-coated ice droplet hydration method". The final sizes of the prepared vesicles were comparable to the original emulsion droplet sizes. This means that the size of vesicles can be controlled by controlling the size of original water droplets of the W/O emulsions. Furthermore, calcein as a hydrophilic fluorescent marker and biopolymers, such as enzyme and polysaccharide, were entrapped into the internal water phases of vesicles. The method proposed in this study enables the formation of vesicles with a controlled size and high entrapment yields, potentially useful for expanding the application fields of vesicles as biocompatible carriers and micro- and nano-reactors for biochemical reactions.