Separation of water from a water-acetone solution was carried out by a pervaporation method using a hydrophilic slilcalite-1 membrane. Silicalite-1 nanocrystals were piled up on the outer surface of cylindrical alumina ceramic filters, followed by a hydrothermal synthesis to form a silicalite-1 protection 5 layer on the nanocrystal layer. In other words, the membrane consisted of a silicalite-1 nanocrystal layer and a silicalite-1 protection layer (the nanocrystal-layered membrane). In order to achieve high hydrophilic properties of the membrane with the remaining silanol group, the liquid-phase oxidation technique was applied to remove the template. From the SEM observation, the nanocrystal layer and the protection layer were clearly observed, and the silicalite-1 protection layer was uniformly formed on the 10 nanocrystal-layer. Pervaporation experiments to separate water from the water-acetone solution were conducted using the nanocrystal-layered membrane. It was considered that the secondary growth of the nanocrystals around the interface between the nanocrystal and protection layers affected the separation properties. The effects of the nanocrystal size on the separation properties were examined. The membrane exhibited selective permeation as well as a high flux of water, and these properties were improved with a 15 decrease in the size of the nanocrystals. Moreover, the layered membrane exhibited high hydrophilic properties regardless of the acetone concentrations.