A systematic study of the high-temperature structural stability is reported for the following three nanolayered composites: (1) MoSi2–MoSi2Nx, (2) Mo–MoSi2Nx, and (3) Mo–MoSi2Nx–MoSi2, where x∼3–4. The alternating layers with layer thickness varying from 1 to 50 nm were synthesized by sputtering techniques. The structural evolution in these composites has been studied by cross-sectional transmission electron microscopy as a function of annealing temperature. As-deposited Mo layers exhibit nanocrystalline structure, while the other types of layers are amorphous in structure. With increasing annealing temperature, MoSi2 crystallizes to form a metastable C40 phase at ∼500 °C and then transforms to the stable C11b phase at ∼900 °C, while MoSi2Nx remains amorphous up to temperature as high as 1000 °C. No difference in crystallization behavior was observed for the constituents in either single phase or multilayered form. One way to improve the toughness of MoSi2 is through the addition of a ductile phase, e.g., Mo. However, the Mo and MoSi2 layers react and the layer structure deteriorates. Previous study has shown that the compound, MoSi2Nx, stays amorphous at 1000 °C. This suggests that it could function either as a stable second-phase reinforcement or as a diffusion barrier between Mo and MoSi2. The MoSi2–MoSi2Nx, Mo–MoSi2Nx, and Mo–MoSi2–MoSi2Nx nanolayers are found to remain stable up to 900 °C (highest temperature tested).