Formation and growth of iron nuclei on the (001) surface of Fe1-xO by hydrogen ion bombardment were observed using scanning tunneling microscope (STM) and low energy electron diffraction (LEED) in order to understand the change in the nano-level structure of the Fe1-xO surface at the initial stage of reduction. It has been found from the STM images that prior to the formation of iron nuclei, hydrogen ion bombardment increases the number of large dents called "depression" on the terrace of the Fe1-xO surface, which may imply that O atoms are deficient on the surface. Simultaneously, the number of steps on the Fe1-xO surface increases probably owing to the reconstraction of the surface structure. According to the LEED pattern, the (2×2) long range periodic structures have appeared which may also demonstrate that the O atom-deficient surface is produced by hydrogen ion bombardment. As the reduction proceeds, the iron nuclei with the shape of a slightly rounded truncated four-sided pyramid are preferentially formed on the surface area where the steps are densified. The side length and the height of the pyramids are 4-8 nm and 1.2-1.8 nm, respectively. Subsequently, the iron nuclei are also formed on the terraces.