The growing demand for pure deuterium (D2) and the need to manage nuclear wastewater have driven research into more efficient hydrogen isotope separation technologies. Quantum sieving techniques, such as Kinetic Quantum Sieving (KQS) and Chemical-Affinity Quantum Sieving (CAQS), have been proposed as alternatives to conventional, energy-intensive methods. However, commercially viable technologies remain undeveloped. In this study, we synthesized Na-GIS-type zeolites (NG zeolites) and Cu-exchanged Na-GIS-type zeolites (CNG zeolites) with a flexible framework and narrow pore size to explore the potential of structural variations for hydrogen isotope separation. The Cu-ion exchange significantly improved the desorption temperature and overall performance, especially for D2 uptake. At 25 K, 100 mbar, and 10 min, CNG zeolite showed a separation factor of 11.56 (2.23 mmol/g), outperforming NG zeolite with a separation factor of 4.74 (1.13 mmol/g). Furthermore, NG zeolite exhibited a synthesis cost of £57,075 per gram and a space–time yield of 9.72 × 10−2 g/(day·m3), demonstrating its potential for commercial application. This research highlights the promise of using zeolite structural variations for scalable and economically viable hydrogen isotope separation.