The effects of atomic hydrogen (H) on formation of In(Ga)As quantum dots (QDs) by self-organizing process have been investigated. The low size fluctuation and uniform-shaped QDs are obtained at growth temperature above 450°C. The average size of InGaAs QDs are decreased from 40 nm to 20 nm by atomic H irradiation. The InGaAs QDs are formed uniformly on growth surface in with-H condition while preferentially formed and distributed along the step edges in without-H case. The photoluminescence (PL) peak intensities and full width at half maximum (FWHM) are also improved by atomic H irradiation. The waiting time before GaAs cap layer deposition is a important factor on the optical properties of QDs.