The effect of the chemical modification of Ge(1 00) semiconductor surfaces on their electronic structure was studied using density functional theory calculations. We have considered various possible adsorption configurations of phenylthiol molecule on Ge(1 0 0) with different spatial orientations relative to the dimer row. The most favorable configuration is that the H-dissociated phenylthiol molecule is located at the inter-dimer site with the covalent bonding between sulfur atom of H-dissociated phenylthiol molecule and down-Ge atom. Simulated STM images of the adsorption configurations reflect the change of the electronic charge density and agree well with the adsorption features observed in the experiment. The projected density of states of the germanium and the phenylthiol molecule could explain the change in surface electronic structures upon chemical adsorption. Moreover, organic functionalization affects the electronic structure like band gap. Band structure analysis shows that the different adsorption configurations of phenylthiol molecules could modify the band gap of clean Ge (1 0 0) surfaces.