Breathing of MIL-53(Al), a flexible metal–organic framework (MOF), leads to dynamic changes as narrow pore (np) transition to large pore (lp). During the flexible and reversible transition, the pore apertures are continuously adjusted, thus providing the tremendous opportunity to separate mixtures of similar-sized- and similar-shaped molecules that require precise pore tuning. Herein, for the first time, we report a strategy for effectively separating hydrogen isotopes through the dynamic pore change during the breathing of MIL-53(Al), representative of flexible MOF. The experiment shows that the selectivity for D₂ over H₂ is strongly related to the state of the pore structure of MIL-53(Al). The highest selectivity (S_D2/H2 = 13.6 at 40 K) was obtained by optimizing the exposure temperature, pressure, and time to systematically tune the pore state of MIL-53(Al).