Dehumidification in CO adsorptive separation processes is an important issue, owing to its high energy consumption. However, available adsorbents such as low-silica zeolites show a significant decrease in CO adsorption capacity when water vapor is present. A core-shell-structured MFI-type zeolite with a hydrophilic ZSM-5 coated with a hydrophobic silicalite-1 shell layer was applied in CO adsorptive separation under wet conditions. This hybrid material demonstrated remarkably high water tolerance with stable CO adsorption performance without additional thermal treatment for regeneration, whereas a significant decrease in the CO adsorption amount because of water vapor was observed on the parent ZSM-5. The core-shell structure of zeolites with high pore volumes, such as LTA or CHA, could also be suitable candidates for high CO adsorption capacity and high water tolerance for practical applications.