The Mo-Si-N single layer and multilayer films were fabricated by a reactive radio frequency, r.f., magnetron sputtering system with pure Mo and Si targets. The Ar/N-2 flow ratio was fixed at 12/8, while r.f. input powers for Mo and Si were 135 W and 0 to 150 W, respectively. The corresponding Si contents in the coating ranged from 0 to approximately 20 at.%. The microstructure of the Mo-Si-N single layers evolved from Mo2N (111) crystalline to amorphous feature with input powers and related Si doping amounts. The Mo-Si-N multilayer coatings were fabricated with crystalline Mo-N, crystalline and amorphous Mo-Si-N layers with sequential stacking of any two building layers. The multilayer film made of Mo-N and crystalline Mo-Si-N layers showed an obvious crystalline microstructure, while the amorphous Mo-Si-N layer incorporated multilayer Mo-Si-N systems effectively suppressed the continuity of the columnar growth. The correlation between mechanical properties, including hardness, Young's modulus, indentation cracking, and scratch behavior, were investigated and discussed in terms of film microstructure evolution.