We prepared silicon nanocrystallites by pulsed laser ablation (PLA) of a Si target in hydrogen background gas. A mixture of hydrogen and helium was used as a background gas and the hydrogen partial pressure was varied. The deposited nanocrystal-film system shows a hierarchical structure composed of surface hydrogenated silicon nanocrystallites as the primary structure and aggregates of the nanocrystallites as the secondary structure. The size of the primary particles was not sensitive to the hydrogen partial pressure, while the porosity of the secondary structure constituted by the aggregation of the primary particles increased with increasing hydrogen partial pressure. This indicates that the surface is stabilized and that aggregation of the primary structure is depressed by surface hydrogenation. The optical gap energy of the deposits shifted to higher energy with increasing hydrogen partial pressure due to the formation of well-isolated nanocrystallites by surface stabilization. These results indicate that PLA in hydrogen gas is a promising technique to prepare surface stabilized and controlled silicon nanocrystallites.