Molecular dynamics simulations are used to investigate the influences of pre-existing microstructural defects on the strength and deformation mechanisms in Ag nanowires under both uniaxial deformation and nanoindentation. In particular, the synergistic effects from both internal and external structural defects, including twin boundaries, surface facets, and a special surface groove, are studied. It is found that the yielding modes vary among Ag nanowires when different microstructures are present. Furthermore, while fivefold twin boundaries are found to cause significant strain hardening under nanoindentation, they can either decrease or increase the initial yield stress of Ag nanowires under uniaxial deformation. The surface groove, in addition, will result in damping behavior of the Ag nanowire that leads to peculiar oscillating load–displacement responses under nanoindentation.