The thermal stability of nickel monosilicide (NiSi) is one of the important research topics in the area of nano-complementary metal oxide semiconductor. This paper reports the effect of germanium (Ge) ion implantation on the thermal stability of the NiSi/Si structure. High dose Ge ion implantation (>5× 1015 cm-2) can improve the thermal stability of the NiSi/Si structure. Ge ion implantation before NiSi formation results in a very smooth NiSi/Si interface due to Ge atom pileup at the NiSi/Si interface. This high concentration Ge layer reduces the interface energy so that the thermal stability can be improved. Both the phase-transformation temperature and agglomeration temperature are improved by 50-100°C. The effects of Ge ion implantation on the NiSi-contacted n+ -p and p+ -n shallow junctions are also examined. Although fast Ni diffusion via the ion implantation induced defects is observed, better thermal stability can still be observed on the n+ -p junction.