The present invention relates to a method of controlling a defect structure in a chabazite (CHA) zeolite membrane, the CHA zeolite membrane having a controlled defect structure by the method and a method of separating CO2, H2, or He and water from a mixture of water and an organic solvent using the CHA zeolite membrane, and more particularly, to a method of controlling a defect structure in a CHA zeolite membrane that improves the separation performance by reducing the amount and size of defects formed in the CHA membrane structure when removing organic-structure-directing agents in the membrane through calcination at a low temperature using ozone.