A three-dimensional microporous thorium-based metal-organic framework (Th-BPYDC-I) that features a suitable pore size for Xe was prepared. The pore confinement effect enables high Xe uptake (2.15 mmol g-1) and good Xe/Kr selectivity (7.49). This work highlights the critical role of the size-matching rule in noble gas separation and provides an alternative option for Xe/Kr separation.