In this paper, we show the effect of atomic hydrogen (H) irradiation on the fabrication of InGaAs quantum dots (QDs) by self-organization process in molecular beam epitaxy. The size of QDs decreased by atomic H irradiation. The high density InGaAs QDs are formed uniformly by atomic H irradiation, while they are distributed mainly along the step edges without H irradiation. On the other hand, atomic H irradiation also improved photoluminescence (PL) properties. PL intensity increase and line width decrease were observed with atomic H irradiated samples. In addition, we fabricated InGaAs QDs on GaAs(311)B substrate. The ordered structures of QDs were obtained on this surface, and the effects of atomic H irradiation were also observed in growth.