Although molecular and quantum sieving (MS and QS) effects have been realized and employed to execute separation tasks, however, little is known about the coexistence of both effects in a compound and its corresponding structure. In this work, we show the first observation of coexistence of both quantum and molecular sieving effects in a [Th6Co2] cage-based compound (Th-Co-Cage-1). The [Th6Co2] cage shows 0.78 nm aperture but with an irregular crescent-like window. This allows [Th6Co2] cage to give ultrahigh uptake for hydrogen isotope and selectivity towards D2 over H2, leading to complete hydrogen isotope separation, as evidenced by experimental breakthrough test. When the size of guest molecule is more than the crescent-like window, a highly rare robust-flexible adsorption was observed, consequently leading to complete isomer separation for C4 and C6 isomers through molecular sieving effect. High thermal, water and chemical stability further supports the materials for practical separation application. The results open up a gate of material with coexistence of QS and MS effects and its fundamental design for superior separation application.