The crystallization behavior of Si3N4 modulation layers in the multilayers and its influences on the microstructure and mechanical properties of ZrN/Si3N4 multilayers were studied. ZrN/Si3N4 multilayers with different Si3N4 thickness were synthesized by reactive magnetic sputtering. The microstructure of the multilayers was characterized with X-ray diffraction and high-resolution transmission electron microscopy, and a nanoindentor was introduced to measure their mechanical properties. The results show that when the thickness is less than 0.9 nm, Si3N4, normally amorphous in the deposited state, could form a NaCl-type pseudocrystal structure due to the template effect of ZrN crystal layer. Crystallized Si3N4 layers and ZrN template layers grow epitaxialy into columnar crystals. Correspondingly, the hardness of the films was enhanced, showing a superhardness effect. Further increasing Si3N4 layer thickness, the coherent interfaces of the multilayers were damaged and Si3N4 layers become amorphous, accompanied by the decline in the hardness of the films.