We studied the effects of the surface hydrogenation on the adsorption, penetration, and silicidation, i.e., the initial reaction processes of the transition-metal Ni and Ti adatoms on the Si surfaces by the first-principles theoretical calculations. We found for both Ni and Ti that the surface hydrogenation changes the most stable surface site and reduces the adsorption energy. In addition, it blocks the penetration, and thus prevents the silicidation. Furthermore, we newly propose its interesting effects from our results, i.e., impurity metal atoms existing in the Si subsurface are extracted onto the surface by the surface hydrogenation. Thereby, highly pure and atomically flat Si surfaces are expected to be obtained.