We exploited the oxide shell structure to explore the structure confinement effect on the nickel silicide growth in one-dimensional nanowire template. The oxide confinement structure is similar to the contact structure (via hole) in the thin film system or nanodevices passivated by oxide or nitride film. Silicon nanowires in direct contact with nickel pads transform into two phases of nickel silicides, Ni31Si12 and NiSi2, after one-step annealing at 550 °C. In a bare Si nanowire during the annealing process, NiSi2 grows initially through the nanowire, followed by the transformation of NiSi2 into the nickel-rich phase, Ni31Si12 starting from near the nickel pad. Ni31Si12 is also observed under the nickel pads. Although the same phase transformations of Si to nickel silicides are observed in nanowires with oxide confinement structure, the growth rate of nickel silicides, Ni31Si12 and NiSi2, is retarded dramatically. With increasing oxide thickness from 5 to 50 nm, the retarding effect of the Ni31Si12 growth and the annihilation of Ni2Si into the oxide confined-Si is clearly observed. Ni31Si12 and Ni2Si phases are limited to grow into the Si/SiOx core-shell nanowire as the shell thickness reaches 50 nm. It is experimental evidence that phase transformation is influenced by the stressed structure at nanoscale.