We discuss the dominant mechanism of strong Fermi-level pinning (FLP) at common element metal/germanium (Ge) interfaces focusing on electronic and bonding structure of semiconductor side. Although epitaxially grown silicon-germanium (SiGe) substrates have many dislocations and defects as well as a natural disorder of atomic bonding structure, the FLP at metal/SiGe interface is much weaker than that at the metal/Ge interface. Additionally, metal/Ge interface with amorphous Ge layer exhibits a significant shift of pinning level. These results consistently support that the strong FLP at common element metal/Ge interface is dominantly caused by intrinsic FLP mechanism like metal-induced gap states.