A nanotemplate of Si bicrystal was fabricated by wafer bonding. The surface electronic energy arrangement on the surface of the Si bicrystal has been measured by scanning tunneling microscopy. The stress effect on the stepped growth of titanium silicide nanorods on Si bicrystal was observed in an ultrahigh vacuum transmission electron microscope in real time. The growth behavior of the nanorods was found to be affected by the underlying dislocation arrays significantly. For a dislocation interspacing of 3.1 nm, the dislocation arrays confined the shape of the nanoclusters and nanorods. Compared to the time of the nanorod remaining at the same length, the elongating time is more than two orders of magnitude shorter. The stepped growth behavior is attributed to the stress contour of the surface strain induced by the underlying dislocation network. This study is constructive to the basic understanding of the stress effect on the initial stage of the reaction of metals on Si and the observation may be applied to nanostructure growth for future applications and design.