The influence of hydrogen contamination on the atomic geometry of Ru(0001) surface was studied by using the density-functional theory and the projector-augmented wave (PAW) method. Based on the optimized structural parameters of hcp Ru from the PAWtotal energy calculation, the surface relaxation, surface energy, and work function of clean Ru(0001) surface were calculated in the same way. The adsorption geometries and total energies of several coverages of hydrogen on Ru(0001) surface including p(1×1), p(1×2), (3^(1/2)×3^(1/2))R30°, and p(2×2), were studied for the hcp and fcc site absorptions combined with the both sites occupation in p(1×1) structure. These results suggested that the Ru(0001) p(1×1)-H geometry had the largest energy gain among all these conformations, so under the condition of low coverage and low H2 pressure, the most possible conformation was p(1×1)-H adsorption. The shrink of Ru(0001) surface with H contamination was -3.7%fromavailable experiments and this work yields -1.11%for hcp and -1.55% for fcc adsorption geometries. It was deduced that the most possible adsorption configuration for a hydrogen contaminated Ru(0001) surface was a mixture of hcp and fcc adsorptions. For a clean Ru(0001) surface the surface contraction was calculated to be near -3.9%, while the experimental measurement predicted -1.9%. This observation implied that even for a“clean”Ru (0001) surface there was still about 13.6%of surface area covered with hydrogen adsorption. These results reflected that the hydrogen contamination could affect the Ru(0001) surface structure dramatically. Furthermore the present study could yield a conclusion naturally that the shrink of the Ru(0001) surface would be reduced with the increase of H atomadsorption below 1.0 ML (monolayer).