This work develops a method for growing Ni-silicide/Si heterostructured nanowire arrays by glancing angle Ni deposition and solid state reaction on ordered Si nanowire arrays. Samples of ordered Si nanowire arrays were fabricated by nanosphere lithography and metal-induced catalytic etching. Glancing angle Ni deposition deposited Ni only on the top of Si nanowires. When the annealing temperature was 500°C, a Ni3Si2 phase was formed at the apex of the nanowires. The phase of silicide at the Ni-silicide/Si interface depended on the diameter of the Si nanowires, such that epitaxial NiSi2 with a {111} facet was formed at the Ni-silicide/Si interface in Si nanowires with large diameter, and NiSi was formed in Si nanowires with small diameter. A mechanism that is based on flux divergence and a nucleation-limited reaction is proposed to explain this phenomenon of size-dependent phase formation.