Solid supports are crucial in heterogeneous catalysis due to their profound effects on catalytic activity and selectivity. However, elucidating the specific effects arising from such supports remains challenging. We selected a series of metal-organic frameworks (MOFs) with 8-connected Zr6 nodes as supports to deposit molybdenum(VI) onto to study the effects of pore environment and topology on the resulting Mo-supported catalysts. As characterized by X-ray absorption spectroscopy (XAS) and single-crystal X-ray diffraction (SCXRD), we modulated the chemical environments of the deposited Mo species. For Mo-NU-1000, the Mo species monodentately bound to the Zr6 nodes were anchored in the microporous c-pore, but for Mo-NU-1008 they were bound in the mesopore of Mo-NU-1008. Both monodentate and bidentate modes were found in the mesopore of Mo-NU-1200. Cyclohexene epoxidation with H2O2 was probed to evaluate the support effect on catalytic activity and to unveil the resulting structure-activity relationships. SCXRD and XAS studies demonstrated the atomically precise structural differences of the Mo binding motifs over the course of cyclohexene epoxidation. No apparent structural change was observed for Mo-NU-1000, whereas the monodentate mode of Mo species in Mo-NU-1008 and the monodentate and bidentate Mo species in Mo-NU-1200 evolved to a new bidentate mode bound between two adjacent oxygen atoms from the Zr6 node. This work demonstrates the great advantage of using MOF supports for constructing heterogeneous catalysts with modulated chemical environments of an active species and elucidating structure-activity relationships in the resulting reactions.