The structural flexibility of nanoporous materials offers a powerful strategy to enhance hydrogen isotope separation via the kinetic quantum sieving (KQS) effect. Unlike rigid frameworks, flexible metal-organic frameworks (MOFs) can dynamically respond to external stimuli, such as pressure, temperature, and guest molecules, enabling selective modulation of pore sizes and diffusion barriers. This review highlights how flexibility modes, including breathing, gate-opening, linker rotation, swelling, and subnetwork displacement, unlock KQS performance by facilitating isotopologue-specific diffusion and adsorption. By surveying recent advances, it is revealed that dynamic structural transformations can extend operational temperature windows, amplify isotope selectivity, and improve uptake capacity. Furthermore, emerging trends such as thermal gating and particle-size-dependent bistability are identified and how the integration of multiple flexibility modes may overcome long-standing limitations of cryogenic isotope separation is discussed. A deeper understanding of structure–function relationships and long-term framework stability will be essential for translating these materials into scalable separation technologies.