An experimental design was applied to the synthesis of AlPO4-21 molecular sieve (AWO structure) by vapor phase transport (VPT) method, using tetramethylguanidine (TMG) as the template. In this study, the effects of crystallization time, crystallization temperature, phosphor content, template content and water content in the synthesis gel were investigated. The materials obtained were characterized by X-ray diffraction, scanning electron microscopy and fourier transform infrared spectroscopy (FT-IR). Microstructural analysis of the crystal growth in vapor synthetic conditions revealed a revised crystal growth route from zeolite AlPO4-21 to AlPO4-15 in the presence of the TMG. Homogenous hexagonal prism AlPO4-21 crystals with size of 7 × 3 μm were synthesized at a lower temperature (120 °C), which were completely different from the typical tabular parallelogram crystallization microstructure of AlPO4-21 phase. The crystals were transformed into AlPO4-21 phase with higher crystallization temperature, longer crystallization time, higher P2O5/Al2O3 ratio and higher TMG/Al2O3 ratio.