Indium (In) catalyzed silicon nanowires were synthesized by the hydrogen radical-assisted deposition method. The In nanoparticles used as catalyst were fabricated from indium oxide film as metal oxide film at various temperatures by hydrogen radical treatment. The sizes of spherical structure were decreased with increasing hydrogen radical treatment temperatures. Moreover, the quantity of smaller nanoparticles was increased. Subsequently, large quantities of Si nanostructures with various crystal diffractions were synthesized on these substrates. The Si nanostructures were observed to be root-like, worm-like and tapered with increasing synthesis temperatures. These results demonstrate that the shapes of Si nanostructure strongly depend on the hydrogen radical treatment temperatures and the growth temperatures. Furthermore, the hydrogen radical treatment for fabricating catalyst nanoparticles and the subsequent deposition method for synthesizing Si nanostructures at various temperatures were proposed and discussed.