Structures of deuterium (D) adsorbed on germanium (001) surface were studied by the density functional theory (DFT) calculations and by the scanning tunneling microscope (STM). Two structures of dihydride adsorption were identified on the Ge (001) surface by STM measurements and confirmed by DFT calculated topographies. Also, differences in structural stabilities were explained based on binding strength differences with Ge and on hybridization effect of the s-orbital of D with the Ge p states. The excitation mode of 0.18 eV observed in the STM dI/dV spectrum was found to correspond to the DFT calculated D-Ge stretching vibration mode of 0.17 eV.