Regularly distributed dislocation networks with a controllable spacing have been formed by wafer bonding. Different kinds of Si bicrystals were fabricated by (001), (111) and (110) Si wafers bonded with (001) silicon-on-insulator (SOI). NiSi2 formed on the bicrystal was found to be affected by the underlying dislocation arrays, confined by the dislocation grids while the surface stress and dislocation density is high enough. It has been demonstrated that through controlling the surface stress arrangement, the shape of the silicide nanostructures can be controlled and various nanostructures can be obtained. This study supports the fundamental understanding of the stress effect on the formation of silicide nanostructures on Si bicrystals and the shape-controlled nanosilicide could be useful for the growth of catalyst-assisted one-dimensional nanostructures.