The understanding of structure-activity relationships at the atomic level has played a profound role in heterogeneous catalysis, providing valuable insights into designing suitable heterogeneous catalysts. However, uncovering the detailed roles of how such active species' structures affect their catalytic performance remains a challenge owing to the lack of direct structural information on a specific active species. Herein, we deposited molybdenum(VI), an active species in oxidation reactions, on the Zr-6 node of a mesoporous zirconium-based metal-organic framework (MOF) NU-1200, using solvothermal deposition in MOFs (SIM). Due to the high crystallinity of the NU-1200 support, the precise structure of the resulting molybdenum catalyst, Mo-NU-1200, was characterized through single-crystal X-ray diffraction (SCXRD). Two distinct anchoring modes of the molybdenum species were observed: one mode (Mol), displaying an octahedral geometry, coordinated to the node through one terminal oxygen atom and the other mode (Mo2) coordinated to two adjacent Zr-6 node oxygen atoms in a tetrahedral geometry. To investigate the role of base in the catalytic activity of these Mo centers, we assessed the activity of Mo-NU-1200 for the aerobic oxidation of 4-methoxybenzyl alcohol as a model reaction. The results revealed that Mo-NU-1200 exhibited remarkably higher catalytic reactivity under base-free conditions, while the presence of base inhibited the catalytic reactivity of this species. SCXRD studies revealed that the molybdenum binding motifs (structures of the supported metal on the Zr-6 node in the MOF) changed over the course of the reactions. Following the oxidation without base, both pristine coordination modes (Mol and Mo2) evolved into a new coordination mode (Mo3), in which the molybdenum atom coordinated to two adjacent oxygen atoms from the Zr-6 node in an octahedral geometry, while in the presence of base, the pristine Mol coordination mode evolved entirely into the pristine Mo2. This study demonstrates the direct observation of an active species' structural evolution from metal installation to subsequent catalytic reaction. As a result, these subtle structural changes in catalyst binding motifs led to distinct differences in catalytic activities, providing a compelling strategy for elucidating structure-activity relationships.