Regularly distributed dislocation network with a controllable spacing could be formed by wafer bonding. Different kinds of Si bicrystals were fabricated by (001), (111) and (110) Si wafers bonded with (001) SOI. NiSi2 formed on the bicrystal was found to be affected by the underlying dislocation arrays. The nanostructures were confined by the dislocation grids. It demonstrates that by means of controlling the surface stress arrangement, the shape of the silicide nanostructures could be controlled and a variety of nanostructures could be obtained. The observation is conductive to the basic understanding of the stress effect on the formation of the silicide nanostructures on Si bicrystals.