Three polymorphic forms of the molybdenum- (VI) complex [MoO2(L)(EtOH)] (1α, 1β, and 1γ) (L2− = 4- methoxy-2-oxybenzaldehyde isonicotinylhydrazonate) were synthesized by the reaction of H2L with the dioxobis- (acetylacetonato)molybdenum(VI) complex, [MoO2(acac)2], in ethanol. Removal of the coordinated ethanol molecule upon grinding or heating led to the solid-state transformation of the polymorphs 1α, 1β, or 1γ into the coordination polymer [MoO2(L)]n (2a). The square inclusion complex [MoO2(L)]4⊃CH2Cl2·4CH2Cl2 (2b⊃CH2Cl2·4CH2Cl2) was obtained by a self-assembly reaction in dichloromethane. Standard Gibbs energies of binding for molybdenum(VI) compounds [MoO2(L)(D)] with the sixth coordination site occupied by a nitrogen or an oxygen donor D were estimated using quantum chemical calculations. Crystal and molecular structures of the molybdenum(VI) compounds [MoO2(L)(EtOH)] (1α, 1β, and 1γ), [MoO2(L)]4⊃CH2Cl2·4CH2Cl2 (2b⊃CH2Cl2·4CH2Cl2), [MoO2(L)(γ-pic)]·γ-pic (3·γ-pic), [MoO2(L)(py)] (4), and [MoO2(L)(DMSO)] (5) were determined by the single crystal X-ray diffraction method. The compounds were further characterized by chemical analysis, thermogravimetric, and differential scanning calorimetry measurements, IR, UV−vis, one- and two-dimensional NMR spectroscopies, and the powder X-ray diffraction method.