Gradient nano-grained (GNG) metals have shown high synergetic strength and good ductility due to their unique gradient microstructure. In this study, the mechanical behavior of gradient nano-grained metals was investigated by three-dimensional discrete dislocation dynamics. The simulation results show a trend that the successive yielding and gradual “transmission” of dislocations along the gradient direction result in a gradient distribution of stress and plastic strain. The distribution of geometrically necessary dislocations is more inhomogeneous in the gradient nano-grained (GNG) sample compared with those homogenous counterparts. The non-uniform deformation response of component layers induces the synergetic-deformation-induced (SDI) strengthening in the GNG sample. The back stress originates from geometrically necessary dislocations that pile up near the interface of gradient layers and leads to a significant hardening while there is a slight softening in different gradient layers in the GNG sample. This study provides a deeper insight into the SDI strengthening in gradient structure from the submicron scale.