A fully ordered noncentrosymmetric barium molybdenum oxyfluoride, α-BaMoO2F4, has been synthesized by a hydrothermal reaction at 200 °C in a concentrated hydrofluoric acid solution. A centrosymmetric polymorph with O/F disorder, β-BaMoO2F4, has been obtained in several minutes when the reaction mixture was stirred at room temperature in the same medium. Interestingly, we found that the metastable β-BaMoO2F4transforms into the thermodynamically stable α-BaMoO2F4in an ambient condition. More detailed kinetic studies using powder X-ray diffraction indicate that the MoO2F4octahedra in the kinetic phase, β-BaMoO2F4, rearrange through the constant dissolution/precipitation process to find a more stable orientation and form the fully ordered α-BaMoO2F4. Density functional theory (DFT) calculations suggest that the formation of the thermodynamically stable α-BaMoO2F4is driven by the strong Mo–O π-interactions induced by Ba2+cations. The new finding on the understanding of the kinetics of solid-state reactions suggests a novel way toward an effective discovery of functional materials with asymmetric structures.