The structural phase of a metal oxide changes with temperature and pressure. During phase transitions, component ions move in multidimensional metal-oxygen networks. Such macroscopic structural events are robust to changes in particle size, even at scales of around 10 nm, and size effects limiting these transitions are particularly important in, for example, high-density memory applications of ferroelectrics. In this study, we examined structural transitions of the molecular metal oxide [Na@(SO3 )2 (n-BuPO3 )4 MoV 4 MoVI 14 O49 ]5- (Molecule 1) at approximately 2 nm by using single-crystal X-ray diffraction analysis. The Na+ encapsulated in the discrete metal-oxide anion exhibited a reversible order-disorder transition with distortion of the Mo-O molecular framework induced by temperature. Similar order-disorder transitions were also triggered by chemical pressure induced by removing crystalline solvent molecules in the single-crystal state or by substituting the countercation to change the molecular packing.