In this paper, the effects of hydrogen in H-MBE (atomic hydrogen-assisted molecular beam epitaxy) have been investigated. We have found that atomic hydrogen is very useful for substrate cleaning in low temperature, surfactant effects such as restrain of island growth and enhancement of layer-by-layer growth, and selective growth on masked substrates. The main mechanism of the selective growth under atomic H irradiation is Ga and As re-evaporation in the form of hydrides from the mask. In addition, atomic hydrogen plays an important role in the achievement of uniformly formed self-organization-quantum dots (QDs) by passivation of surface-step. On the other hand, it has been observed that the enhanced Al re-evaporation from the GaAs(001) substrate arises via formation of Al hydrides during A1GaAs layer growth.