A series of polynuclear, dinuclear, and mononuclear Mo(VI) complexes were synthesized with the hydrazonato ligands derived from 5-methoxysalicylaldehyde and the corresponding hydrazides (isonicotinic hydrazide (H2L1), nicotinic hydrazide (H2L2), 2-aminobenzhydrazide (H2L3), or 4-aminobenzhydrazide (H2L4)). The metallosupramolecular compounds obtained from non-coordinating solvents, [MoO2(L1,2)]n (1 and 2) and [MoO2(L3,4)]2 (3 and 4), formed infinite structures and metallacycles, respectively. By blocking two coordination sites with cis-dioxo ligands, the molybdenum centers have three coordination sites occupied by the ONO donor atoms from the rigid hydrazone ligands and one by the N atom of pyridyl or amine-functionalized ligand subcomponents from the neighboring Mo building units. The reaction in methanol afforded the mononuclear analogs [MoO2(L1-4)(MeOH)] (1a–4a) with additional monodentate MeOH ligands. All isolated complexes were tested as catalysts for cyclooctene epoxidation using tert-butyl hydroperoxide (TBHP) as an oxidant in water. The impact of the structure and ligand lability on the catalytic efficiency in homogeneous cyclooctene epoxidation was elucidated based on theoretical considerations. Thus, dinuclear assemblies exhibited better catalytic activity than mononuclear or polynuclear complexes.