This investigation focused on the thermal stability of nanocrystalline (NC) binary and ternary Ni-Y-Zr alloys synthesized through ball-milling. The microstructural changes following annealing, conducted up to 1200 °C, were studied using various techniques, including X-ray-line-broadening, micro-hardness, and transmission electron microscopy. The results revealed that the rate of grain growth observed in the Ni-Y-Zr ternary alloy at 600 °C resembled that in pure NC-Ni at 100 °C. Moreover, the Ni-1.4Y-1.1Zr ternary system exhibited a maximum hardness of 753 HV (average) at 600 °C, which was approximately 60 HV higher than the Ni-1.2Y/1.9Y and Ni-1.5Zr/2.7Zr binary alloys and more than double that of pure NC-Ni for similar grain sizes. These characteristics were linked to the formation of nano-sized oxides and nitrides of Y and Zr within the microstructure. In summary, this study emphasizes the notable high-temperature microstructure stability of Ni-based ternary alloys, attributed to the additive effects of Y and Zr. Due to this extended stability, this ternary system could find potential applications at elevated temperatures in areas such as jet engine turbine blades and power plants.