Capture and storage of the long-lived ⁸⁵Kr is an efficient approach to mitigate the emission of volatile radionuclides from the spent nuclear fuel reprocessing facilities. However, it is challenging to separate krypton (Kr) from xenon (Xe) because of the chemical inertness and similar physical properties. Herein we prepared high-silica CHA zeolite membranes with ultra-high selectivity and irradiation stability for Kr/Xe separation. The suitable aperture size and rigid framework endures the membrane a strong size-exclusion effect. The ultrahigh selectivity of 51–152 together with the Kr permeance of 0.7–1.3×10⁻⁸ mol m⁻² s⁻¹ Pa⁻¹ of high-silica CHA zeolite membranes far surpass the state-of-the-art polymeric membranes. The membrane is among the most stable polycrystalline membranes for separation of humid Kr/Xe mixtures. Together with the excellent irradiation stability, high-silica CHA zeolite membranes pave the way to separate radioactive Kr from Xe for a notable reduction of the volatile nuclear waste storage volume.