Morphology of Ag nanocrystals (NCs) is essential to the NC application in catalysis, optics, and as antibacterial agents. Therefore, it is important to develop synthetic methods and understand the evaluation of NC morphology in different chemical environments. In this study, we report interesting findings of the morphological change of fivefold-twinned Ag-Au-Ag nanorods (NRs) under the effect of H2O2 both as an oxidant (etchant) and a reductant. At low H2O2 concentration, the reconstruction of Ag-Au-Ag NRs was dominated by the growth along the longitudinal direction of NRs. With the increase of H2O2 concentration, the reconstruction also occurs in the transverse direction, and a clear change in particle morphology was observed. We further systematically studied the mechanism of the reaction. The results showed that the transition of the morphology was a two-step process: (1) the etching of Ag on the seeds and (2) the reduction of Ag2O. In the second step, the reaction kinetics was highly affected by H2O2 concentration. At low H2O2 concentration, the growth mainly occurs along ⟨110⟩. However, at high H2O2 concentration, the reduction of Ag was not facet-selective. Using the developed method, we can prepare various bimetallic NCs (high aspect ratio NRs with abundant pinholes, nanoplates, and other NCs). The effect of the reconstruction process on the surface-enhanced Raman scattering (SERS) performance of NCs was investigated.