AlN/SiO2 nanomultilayers with different SiO2 thicknesses were synthesized by reactive magnetron sputtering. X-ray diffraction and high-resolution transmission electron microscopy were used to characterize the microstructure, and nanoindentation technology was used to measure the mechanical properties of the multilayers. The crystallization of SiO2 as well as its influences on the growth and mechanical properties of the multilayers was studied. Results showed that due to the template effects of hcp AlN, amorphous SiO2 was forced to crystallize to a hcp pseudocrystal structure when its thickness was below 0.6 nm. The SiO2 epitaxially grew with AlN in the multilayer with coherent interfaces. At this time, a tensile and compressive alternate stress field was developed corresponding to the modulation structure. The hardness of the multilayers was enhanced as a result. Calculation revealed that alternate stress field played an important role in multilayers’ reinforcement. As thickness increases, SiO2 grew into amorphous again, resulting in the blockade of epitaxial growth in the multilayers and disappearing of the hardness enhancement.