Anodic aluminum oxide (AAO) films with uniform cylindrical pores are widely used as templates and membranes. The annealing of initially amorphous AAO enhances its chemical stability, but simultaneously changes its morphology and phase composition. Here we study the effect of annealing in the temperature range up to 1150 °C on structural and phase transitions in porous AAO films prepared by Al anodization in oxalic acid. Full-profile analysis of high-resolution X-ray diffraction patterns using the Rietveld method reveals the sequence of phase transformations (amorphous alumina → a mixture of γ-Al2O3 and θ-Al2O3 → a mixture of γ-Al2O3, δ-Al2O3, and θ-Al2O3 → α-Al2O3) and is used for quantitative phase analysis. Decomposition of oxalate-impurities, induced by the AAO crystallization, is studied using combined Fourier-transform infrared spectroscopy and thermogravimetry analysis. The removal of impurities results in the formation of mesopores in the AAO cell walls with a consequence increase in the specific surface area up to 80 m2·g− 1. The apparent activation energies of the removal of water (~35 kJ·mol− 1) and of the decomposition of carbon-containing impurities (~350 kJ·mol− 1) are calculated. Morphology-dependent kinetics of the impurities removal is described in the framework of the limited mass-transport of oxalate decomposition products through the cell walls.