A technique is developed to control the chemical reactivity of a silicon single‐crystal surface through chemical modification with atomic hydrogen. The reactivity of the reconstructed single‐crystal surface prepared by high‐temperature treatment in an ultrahigh vacuum is significantly decreased by capping the dangling bonds of top‐layer silicon atoms with hydrogen atoms. The Si—H bonds on the hydrogenated surface are found to be much more stable against oxidation than the Si—Si back bonds. The hydrogen‐passivated silicon surface is reactivated by electron beam irradiation. An ultrathin oxide layer pattern can be prepared using preferential oxidation of the area reactivated by a focused electron beam.