Aluminium anodizing in phosphonic acid is known to produce anodic aluminium oxide (AAO) honeycomb structures with large interpore distances. However, detailed information on two-stage anodizing in phosphonic acid and annealing conditions required for the crystallization of AAO cell walls have not been reported yet. Here, the kinetics of aluminium anodizing in 1 M phosphonic acid and the thermal behaviour of the resulting AAO have been studied in detail. The apparent activation energy of aluminium anodizing is 65 kJ mol–1 and the AAO growth rate reaches 15 µm h–1 before oxide burning. A universal approach for stable two-stage anodizing at high voltages allowing to prevent porous structure rearrangement in the upper part of AAO is proposed. It involves the preliminary formation of a dense barrier alumina layer by anodizing in a weak acid electrolyte before the second anodizing step in phosphonic acid. The crystallization pathways of AAO obtained in phosphonic acid electrolyte are revealed based on differential scanning calorimetry, X-ray diffraction, and solid-state nuclear magnetic resonance techniques. The designed annealing program allows one to preserve the honeycomb porous structure after the crystallization of AAO in corundum at 1310°C for 60 h. AAO obtained in phosphonic acid possesses high thermal stability and, thus, is promising as a support for gas sensors and fuel cells.