Owing to the diffusion of Si elements towards the metal substrate and the “pesting” behavior caused by volatilization of MoO3, magnetron-sputtered MoSi2 coating is highly susceptible to failure and unable to protect the metal substrate from oxidation. In this work, therefore, an MoSi2(N) interlayer was sputtered on Mo substrates as the diffusion barrier, followed by deposition of Si-doped MoSi2 (i.e., MoSi2(Si)) layer to suppress the “pesting” behavior. The as-deposited coatings were annealed subsequently at 1000 °C in an Ar atmosphere to obtain a stable structure. To evaluate the oxidation resistance, the annealed coating was heated in a muffle furnace in air at 700 °C, 1000 °C and 1200 °C for different durations. The coating structure, surface morphology, cross section and chemical composition were examined by X-ray diffraction, field emission scanning electron microscopy, and energy dispersive spectroscopy. The results showed the MoSi2(N) interlayer was amorphous and kept the most stable thermal stability at Ar/N2 flow rate of 20/20 sccm. It effectively blocked the downward diffusion of Si. Free state Si elements only diffused towards the coating surface. “Pesting” pores in the MoSi2(Si) layer were repaired by the growth of SiO2 layer via the preferential oxidation of Si. The mechanism for the enhanced oxidation resistance was explained through a model.