The surface composition of Ge/Si(001)2×1 surfaces after atomic hydrogen (H) irradiation was investigated using IR reflection spectroscopy in UHV. It was observed that H irradiation at room temperature causes etching of the surface Ge layer. However, when H is irradiated at elevated temperatures, the etching reaction does not occur. Instead, Ge at the surface moves into the subsurface region and Si atoms tend to exist on the topmost surface as monohydrides of mixed Ge-Si and pure Si-Si dimer structures. This behavior is remarkably different from that of Ge/Si(001) surfaces in absence of hydrogen, where Ge is segregated at the surface and forms Ge-Ge pure dimers. First-principles total energy calculations indicates that the presence of hydrogen reverses the stability of the surface composition from Ge to Si, in good agreement with the experimental results.