Monolithic AlN，Si3N4 films and AlN/Si3N4 multilayers with different modulation periods were prepared by reactively magnetic sputtering. The films were characterized by X-ray diffraction, high-resolution transmission electron microscopy and nanoindentation. The results showed that the crystal structure of Si3N4 layers in the multilayers and the hardness of AlN/Si3N4 multilayers depend on the thickness of Si3N4 layer. When the thickness of AlN is 4.0nm and that of Si3N4 layer is 0.4nm, Si3N4 layers grew epitaxially with AlN and form strong columnar crystals which extend over several modulation periods. A large degree of hardness enhancement of the multilayer was produced. The microstructure of Si3N4 changes from crystalline to amorphous as Si3N4 thickness increases, leading to blocking of the epitaxial growth and the superhardness effect disappears. The critical thickness of Si3N4 layers, which marks the change from crystalline to amorphous, has been calculated through thermodynamic and elastic considerations. The hardening mechanisms of AlN/Si3N4 multilayers are discussed.