A series of large-scale molecular dynamics simulations have been performed to investigate the tensile properties and atomistic deformation mechanisms for the nanostructured Cu with three typical microstructures: the hierarchical structure consisting of both twin-free grains (d = 70 nm) and grains with bundles of smaller nanotwins (d = 70 nm, λ = 10 nm), the fully nanograined structure and the fully nanotwinned structure. The average flow stress of the hierarchically structure is found to be higher than that calculated by rule of mixture. As compared with that of fully nanograined structure, the strength for the twin-free grains in the hierarchical structure is promoted and gives extra hardening due to the increased dislocation density and dislocation behaviours. It is also found that the nanotwin bundles are more deformable than the twin-free grains in the hierarchical structure according to the deviatoric strain invariant contour. This indicates that the fully nanograined structure cannot only be strengthened to a higher level, but also obtain better ductility by embedded with stronger bundles of smaller nanotwins. Thus, a superior strength–ductility synergy could be obtained in this kind of hierarchical structures, and this novel strategy has also been implemented in bulk austenitic steels or copper by recent experiments.