In this paper, we demonstrated the shallow NiSiGe Schottky junction on the SiGe P-channel by using low-temperature microwave annealing. The NiSiGe/n-Si Schottky junction was formed for the Si-capped/SiGe multi-layer structure on an n-Si substrate (Si/Si0.57Ge0.43/Si) through microwave annealing (MWA) ranging from 200 to 470°C for 150 s in N2 ambient. MWA has the advantage of being diffusion-less during activation, having a low-temperature process, have a lower junction leakage current, and having low sheet resistance (Rs) and contact resistivity. In our study, a 20 nm NiSiGe Schottky junction was formed by TEM and XRD analysis at MWA 390°C. The NiSiGe/n-Si Schottky junction exhibits the highest forward/reverse current (ION/IOFF) ratio of ~3 × 105. The low temperature MWA is a very promising thermal process technology for NiSiGe Schottky junction manufacturing.